Analysis for the ReproPhylo manuscript¶
This notebook containts the analysis conducted for the ReproPhylo manuscript. The repository containig it, as well as related files, is at https://github.com/HullUni-bioinformatics. The ReproPhylo pipeline is needed to run it is provided as a Docker image. The manual and development version is in our Git page GitHub page.
Table of content¶
1 The full unannotates script
2 The same script, with annotations
2.1 Turn a nexus file with PAUP style charset lines into a ReproPhylo Project instance
2.2 Read a supplementary table with pandas
2.3 Manually assign species to clades
2.4 Export all the records to a text file
2.5 Making sure all-gap possitions are removed from the alignments
2.6 Preparing supermatrices from 200 loci long sliding windows along the entrophy gradient
2.6.1 Calculating the statistics
2.6.2 Sort the loci according to statistics values
2.6.3 Figure 2A
2.6.4 Figure S1, Plot a box plot for each parameter and locus
2.7 Prepare the Concatenation objects
2.8 Reconstruct the trees
2.9 Verify the git commit
2.10 Plot the trees, Figure 2A 1-6
2.11 Robinson Foulds like metrics
2.11.1 Figure 2B - Topological
2.11.2 Figure 2C - Branch length
2.11.3 Figure 2D - Proportional
2.12 Prepare zip folder
2.13 Add README and commit
2.14 Manual commit of some additional files
1 The full, unannotated script:¶
The cell bellow contains the full analysis. Default values are not shown.
An annotated version follows. Default values are explicitly indicated there.
In [ ]:
from reprophylo import *
# Read Kawahara_Breinholt_2014 loci and start a Project
nexus_filename = 'data/Kawahara_Breinholt_2014/'+\
'Kawahara_Breinholt_2014_26taxa_465loci_Degen_nt12.nex'
pj = pj_from_nexus_w_charset(nexus_filename, 'data', 'dna', 'CDS', project = True,
pickle = 'szitenberg_et_al_15_reprophylo',git = True)
# manually read metadata with pandas from
# Kawahara_Breinholt_2014 supplementary file
supp3 = 'data/Kawahara_Breinholt_2014/'+\
'rspb20140970supp3.csv'
metadata = pd.read_table(supp3, skiprows=2)
for r in pj.records:
source = r.features[0]
original_id = source.qualifiers['original_id'][0]
record_metadata = metadata.loc[metadata['Sample ID'] == original_id]
record_metadata = record_metadata.to_dict()for key in record_metadata: # This will add each value in the table
source.qualifiers[key] = [record_metadata[key].items()[0][1]]
source.qualifiers['organism'] = source.qualifiers['Taxa']
# Manually assign clades to taxa:
clades = {'Papilio glaucus': 'butterfilies',
'Macrosoma sp.*': 'butterfilies',
'Megathymus yuccae*': 'butterfilies',
'Semomesia campanea': 'butterfilies',
'Danaus plexippus*': 'butterfilies',
'Phyllocnistis citrella*': 'I',
'Plutella xylostella*': 'I',
'Grapholita dimorpha*': 'I',
'Lantanophaga pusillidactyla*': 'I',
'Urodus parvula*': 'I',
'Morpheis mathani*': 'I',
'Megalopyge tharops*': 'I',
'Dalcera abrasa*': 'I',
'Thubana sp.*': 'III',
'Pterodecta felderi*': 'III',
'Zeuzerodes maculata*': 'III',
'Lacosoma ludolpha*': 'IV',
'Lyssa zampa*': 'IV',
'Nothus lunus*': 'IV',
'Nemoria lixaria*': 'IV',
'Anigraea sp.': 'IV',
'Bombyx mori*': 'IV',
'Manduca sexta*': 'IV',
'Artace sp.*': 'IV',
'Myelobia sp.*': 'IV',
'Actias luna*': 'IV'}
pj.add_qualifier_from_source('Taxa')
for taxon in clades:
pj.if_this_then_that(taxon, 'Taxa', clades[taxon], 'Clade')
# Remove all gap positions
trimal = TrimalConf(pj, method_name='no_trim', trimal_commands={'noallgaps': True})
pj.trim([trimal])
# Calculate loci statistics
# (entropy, conservation, gap score, GC content and sequence lengths)
stats = LociStats(pj)
# Sort the loci according to entropy
stats.sort(parameter = 'entropy', reverse = True)
# Plot the loci statistics as boxplots
stats.plot('plots.png', figsize=(15,23), params='all',
lable_fsize=20, xtick_fsize=2, ytick_fsize=1,
boxcolor='salmon',
whiskercolor='gray',
capcolor='black',
mediancolor='white',
medianline_w=3)
# Make concatenations of 200 loci sliding window of entropy
concatenations = stats.slide_loci('source_original_id',
parameter='entropy',
start=0,length=200,step=50)
# Add the concatenation objects to the project
for concat in concatenations:
pj.add_concatenation(concat)
# Create the supermatrices
pj.make_concatenation_alignments()
# And collect their names
aln_names = [c.name for c in pj.concatenations]
# Build the trees
raxml = RaxmlConf(pj, alns=aln_names, threads=6)
# reconstruct the trees
pj.tree([raxml])
# Remove stars from species names
from itertools import chain
for f in chain(*[r.features for r in pj.records]):
if 'Taxa' in f.qualifiers:
f.qualifiers['Taxa'][0] = f.qualifiers['Taxa'][0].replace('*','')
pj.propagate_metadata()
# Plot the trees
pics = {'Bombycoidea': 'silhouettes/Bombycoidea.png',
'Calliduloidea': 'silhouettes/Calliduloidea.png',
'Cossoidea': 'silhouettes/Cossoidea.png',
'Gelechioidea': 'silhouettes/Gelechioidea.png',
'Geometroidea': 'silhouettes/Geometroidea.png',
'Hepialoidea': 'silhouettes/Hepialoidea.png',
'Papilionoidea': 'silhouettes/Papilionoidea.png',
'Mimallonoidea': 'silhouettes/Mimallonoidea.png',
'Zygaenoidea': 'silhouettes/Zygaenoidea.png',
'Lasiocampoidea': 'silhouettes/Lasiocampoidea.png',
'Thyridoidea': 'silhouettes/Thyridoidea.png',
'Pterophoroidea': 'silhouettes/Pterophoroidea.png',
'Pyraloidea': 'silhouettes/Pyraloidea.png',
'Noctuoidea': 'silhouettes/Noctuoidea.png',
'Gracillarioidea': 'silhouettes/Gracillarioidea.png',
'Yponomeutoidea': 'silhouettes/Yponomeutoidea.png',
'Urodoidea': 'silhouettes/Urodoidea.png',
'Tortricoidea': 'silhouettes/Tortricoidea.png'
}
colors = {'Bombycoidea': 'DodgerBlue',
'Calliduloidea': 'DodgerBlue',
'Cossoidea': 'DodgerBlue',
'Gelechioidea': 'DodgerBlue',
'Geometroidea': 'DodgerBlue',
'Hepialoidea': 'DodgerBlue',
'Papilionoidea': 'SaddleBrown',
'Mimallonoidea': 'DodgerBlue',
'Zygaenoidea': 'DodgerBlue',
'Lasiocampoidea': 'DodgerBlue',
'Thyridoidea': 'DodgerBlue',
'Pterophoroidea': 'DodgerBlue',
'Pyraloidea': 'DodgerBlue',
'Noctuoidea': 'DodgerBlue',
'Gracillarioidea': 'DodgerBlue',
'Yponomeutoidea': 'DodgerBlue',
'Urodoidea': 'DodgerBlue',
'Tortricoidea': 'DodgerBlue'}
bg = {'butterfilies': 'LightSkyBlue',
'I': 'PowderBlue',
'III': 'LightGrey',
'IV': 'Beige'
}
supports = { 'DarkBlue' : [100,99],
'DimGray': [99,80]}
dir_name = "butterfly_figs"
html_name = "%s/figures.html"%dir_name
if not os.path.exists(dir_name):
os.mkdir(dir_name)
pj.clear_tree_annotations()
pj.annotate(dir_name, 'mid','mid', ['Taxa'],
leaf_node_color_meta='source_Superfamily',
leaf_label_colors=colors, ftype='Arial Black',
fsize=40, node_support_dict=supports,
support_bullet_size=15, pic_meta='source_Superfamily',
pic_paths=pics, pic_w=85, pic_h=65, node_bg_meta='Clade',
node_bg_color=bg, branch_width=6, branch_color='RoyalBlue',
scale=2500, html=html_name)
# Calculate pairwise tree distances
if not os.path.exists('rf_figs'):
os.mkdir('rf_figs')
# topological
figfile1, legend = calc_rf(pj, 'rf_figs', rf_type='topology', unrooted_trees=True, trees=trees)
# branch-length
figfile2, legend = calc_rf(pj, 'rf_figs', rf_type='branch-length', unrooted_trees=True, trees=trees)
# topological
figfile3,legend = calc_rf(pj, 'rf_figs', rf_type='proportional', unrooted_trees=True, trees=trees)
# Write a zip file
publish(pj, 'report', 'butterfly_figs/',
compare_trees=['topology','branch-length','proportional'],
trees_to_compare=trees)
2 The same script, with annotations¶
In [1]:
from reprophylo import *
In [2]:
nexus_filename = 'data/Kawahara_Breinholt_2014/'+\
'Kawahara_Breinholt_2014_26taxa_465loci_Degen_nt12.nex'
pj = pj_from_nexus_w_charset(nexus_filename,
'data', # path to write intermediate fasta file
'dna', # Character type ('dna' or 'prot')
'CDS', # Feature type (Any)
project = True, # Will return a Project instance instead of a list
# of fasta files per partition
# if project will save it to this file:
pickle = 'szitenberg_et_al_15_reprophylo',
git = True) # Will start and manage repository
/home/amir/Dropbox/python_modules/rpgit.py:74: UserWarning: Thanks to Stack-Overflow users Shane Geiger and Billy Jin for the git wrappers code
warnings.warn('Thanks to Stack-Overflow users Shane Geiger and Billy Jin for the git wrappers code')
/home/amir/Dropbox/python_modules/rpgit.py:90: UserWarning: A git repository was created in /home/amir/Dropbox/Szitenberg_et_al_2015_ReproPhylo.
warnings.warn('A git repository was created in %s.'%repoDir)
/home/amir/Dropbox/python_modules/reprophylo.py:255: UserWarning: The new repository is called szitenberg_et_al_15_reprophylo.
warnings.warn('The new repository is called %s.'%open(cwd + '/.git/description', 'r').read().rstrip())
DEBUG:Cloud:Log file (/home/amir/.picloud/cloud.log) opened
1/465 reading EOG69CQC1_1 2/465 reading EOG6M65NR_1 3/465 reading EOG69KFV8_1 4/465 reading EOG6SN1SH_1 5/465 reading EOG654933_1 6/465 reading EOG66147B_1 7/465 reading EOG6PRSVJ_1 8/465 reading EOG6PRSVH_1 9/465 reading EOG680J15_1 10/465 reading EOG6S7JTK_1 11/465 reading EOG60ZR1Z_1 12/465 reading EOG6DBTJG_1 13/465 reading EOG6FXRCN_1 14/465 reading EOG69ZXTF_1 15/465 reading EOG60P4BD_1 16/465 reading EOG6BCDR6_1 17/465 reading EOG64QT4T_1 18/465 reading EOG6NCMGZ_1 19/465 reading EOG66147D_1 20/465 reading EOG67SSJD_1 21/465 reading EOG6K3M19_1 22/465 reading EOG670TN2_1 23/465 reading EOG60P4BJ_1 24/465 reading EOG6DBTK0_1 25/465 reading EOG647FZH_1 26/465 reading EOG6D5327_1 27/465 reading EOG63TZZV_1 28/465 reading EOG6HDSZD_1 29/465 reading EOG64MXX7_1 30/465 reading EOG68WC5N_1 31/465 reading EOG6GTKHJ_1 32/465 reading EOG68SGXD_1 33/465 reading EOG6G7C30_1 34/465 reading EOG6K6G7Z_1 35/465 reading EOG6SXNH7_1 36/465 reading EOG65X80D_1 37/465 reading EOG6NVZQC_1 38/465 reading EOG6MPHV2_1 39/465 reading EOG6SJ5J4_1 40/465 reading EOG6C87X0_1 41/465 reading EOG68KRFS_1 42/465 reading EOG6GHZSR_1 43/465 reading EOG65493R_1 44/465 reading EOG6868HF_1 45/465 reading EOG666VQ4_1 46/465 reading EOG6MSD2X_1 47/465 reading EOG63FH1T_1 48/465 reading EOG698V44_1 49/465 reading EOG6F7NPM_1 50/465 reading EOG676K3N_1 51/465 reading EOG651DV5_1 52/465 reading EOG6KWJXS_1 53/465 reading EOG6894QQ_1 54/465 reading EOG6868GW_1 55/465 reading EOG69PB31_1 56/465 reading EOG6SJ5JV_1 57/465 reading EOG65492X_1 58/465 reading EOG6JDHBD_1 59/465 reading EOG63212K_1 60/465 reading EOG67H5VB_1 61/465 reading EOG6C87X4_1 62/465 reading EOG61C717_1 63/465 reading EOG673PVJ_1 64/465 reading EOG68D102_1 65/465 reading EOG60ZR1T_1 66/465 reading EOG68WC5K_1 67/465 reading EOG63JC89_1 68/465 reading EOG6CJVMH_1 69/465 reading EOG60VVTB_1 70/465 reading EOG698V46_1 71/465 reading EOG6GHZSZ_1 72/465 reading EOG6J6RV9_1 73/465 reading EOG6S4PM1_1 74/465 reading EOG68D104_1 75/465 reading EOG68KRG8_1 76/465 reading EOG6N8R81_1 77/465 reading EOG63BMSV_1 78/465 reading EOG69KFV1_1 79/465 reading EOG6H1B0Q_1 80/465 reading EOG6CJVMF_1 81/465 reading EOG6C2HF4_1 82/465 reading EOG6CC44S_1 83/465 reading EOG6FXRCK_1 84/465 reading EOG6M65N3_1 85/465 reading EOG6R2400_1 86/465 reading EOG6BK57N_1 87/465 reading EOG68KRG4_1 88/465 reading EOG61C70T_1 89/465 reading EOG6BK575_1 90/465 reading EOG6R506X_1 91/465 reading EOG6SJ5JS_1 92/465 reading EOG6JT09G_1 93/465 reading EOG6HQDPG_1 94/465 reading EOG6H4677_1 95/465 reading EOG63212W_1 96/465 reading EOG6F7NPJ_1 97/465 reading EOG695ZW4_1 98/465 reading EOG61NTQM_1 99/465 reading EOG6SJ5J3_1 100/465 reading EOG6NZTZ3_1 101/465 reading EOG6J3WM7_1 102/465 reading EOG680J16_1 103/465 reading EOG68SGXM_1 104/465 reading EOG60K843_1 105/465 reading EOG65X811_1 106/465 reading EOG602WWN_1 107/465 reading EOG6RNBCT_1 108/465 reading EOG6M39DN_1 109/465 reading EOG63BMSB_1 110/465 reading EOG6RFKXS_1 111/465 reading EOG6RXZ4G_1 112/465 reading EOG6B8JHB_1 113/465 reading EOG67SSJJ_1 114/465 reading EOG654930_1 115/465 reading EOG6PVP2X_1 116/465 reading EOG69GKKW_1 117/465 reading EOG6RXZ3G_1 118/465 reading EOG6NZTXP_1 119/465 reading EOG602WX4_1 120/465 reading EOG6KH2ZX_1 121/465 reading EOG61JZGH_1 122/465 reading EOG6QFWHZ_1 123/465 reading EOG6SJ5J9_1 124/465 reading EOG6STS8H_1 125/465 reading EOG68PMPX_1 126/465 reading EOG6RFKXB_1 127/465 reading EOG62BXD6_1 128/465 reading EOG647FXX_1 129/465 reading EOG6B8JHP_1 130/465 reading EOG6F7NPN_1 131/465 reading EOG6GHZSG_1 132/465 reading EOG6P8FN9_1 133/465 reading EOG6S1TBX_1 134/465 reading EOG6R506R_1 135/465 reading EOG6DFPRT_1 136/465 reading EOG65TCRW_1 137/465 reading EOG6HX54P_1 138/465 reading EOG60VVST_1 139/465 reading EOG65HS25_1 140/465 reading EOG6FFD5C_1 141/465 reading EOG6PNXM9_1 142/465 reading EOG6R506D_1 143/465 reading EOG670TNG_1 144/465 reading EOG6F4SFZ_1 145/465 reading EOG6Q8524_1 146/465 reading EOG6QVCGP_1 147/465 reading EOG669QZR_1 148/465 reading EOG6JT09B_1 149/465 reading EOG65TCRS_1 150/465 reading EOG6CJVMM_1 151/465 reading EOG6K9BH5_1 152/465 reading EOG63N7HX_1 153/465 reading EOG6QRH88_1 154/465 reading EOG6M65N6_1 155/465 reading EOG6JQ426_1 156/465 reading EOG61G385_1 157/465 reading EOG6QRH81_1 158/465 reading EOG6NCMH9_1 159/465 reading EOG6FN4N0_1 160/465 reading EOG65HS1N_1 161/465 reading EOG6CC44T_1 162/465 reading EOG6RJG4W_1 163/465 reading EOG6K9BGH_1 164/465 reading EOG6FR0VW_1 165/465 reading EOG6N8R82_1 166/465 reading EOG6K0QSG_1 167/465 reading EOG6KKZ6X_1 168/465 reading EOG60VVTG_1 169/465 reading EOG6QC198_1 170/465 reading EOG6D26TG_1 171/465 reading EOG6FFD52_1 172/465 reading EOG6QZ7R6_1 173/465 reading EOG6KKZ71_1 174/465 reading EOG634W9K_1 175/465 reading EOG6DNF7N_1 176/465 reading EOG679FBS_1 177/465 reading EOG6BG909_1 178/465 reading EOG63BMSG_1 179/465 reading EOG61RPZF_1 180/465 reading EOG6BVRZ3_1 181/465 reading EOG6MSD3H_1 182/465 reading EOG60CHM6_1 183/465 reading EOG6PC9WG_1 184/465 reading EOG60GCVD_1 185/465 reading EOG6R506Q_1 186/465 reading EOG66MBNX_1 187/465 reading EOG605S4X_1 188/465 reading EOG66HGF2_1 189/465 reading EOG65TCRN_1 190/465 reading EOG608ND4_1 191/465 reading EOG6640GX_1 192/465 reading EOG6SQX12_1 193/465 reading EOG69GKMS_1 194/465 reading EOG6FR0VX_1 195/465 reading EOG6P2Q5K_1 196/465 reading EOG634W9M_1 197/465 reading EOG6B8JHC_1 198/465 reading EOG6QVCGS_1 199/465 reading EOG6Q2DJZ_1 200/465 reading EOG64TPC4_1 201/465 reading EOG6D26TV_1 202/465 reading EOG605S4Z_1 203/465 reading EOG6N04JN_1 204/465 reading EOG6DNF8K_1 205/465 reading EOG68GW71_1 206/465 reading EOG6CC44M_1 207/465 reading EOG63JC8S_1 208/465 reading EOG67WNS9_1 209/465 reading EOG6NS3G8_1 210/465 reading EOG64TPCQ_1 211/465 reading EOG6PNXM6_1 212/465 reading EOG68GW77_1 213/465 reading EOG6NS3GS_1 214/465 reading EOG6229Q2_1 215/465 reading EOG63TZZW_1 216/465 reading EOG6NP76T_1 217/465 reading EOG63JC90_1 218/465 reading EOG67H5V2_1 219/465 reading EOG63R3QZ_1 220/465 reading EOG65QHJ5_1 221/465 reading EOG6MW89D_1 222/465 reading EOG64F6DH_1 223/465 reading EOG6SJ5K0_1 224/465 reading EOG69GKM6_1 225/465 reading EOG66HGFW_1 226/465 reading EOG6MKNM3_1 227/465 reading EOG63V00H_1 228/465 reading EOG6BG90S_1 229/465 reading EOG6NP77P_1 230/465 reading EOG66DM62_1 231/465 reading EOG6JQ41Z_1 232/465 reading EOG6QFWJH_1 233/465 reading EOG69CQBW_1 234/465 reading EOG6N04K4_1 235/465 reading EOG69KFTV_1 236/465 reading EOG6CJVMQ_1 237/465 reading EOG6SBF24_1 238/465 reading EOG6P8FNB_1 239/465 reading EOG62V8KS_1 240/465 reading EOG6DZ204_1 241/465 reading EOG6C5CPH_1 242/465 reading EOG6FFD51_1 243/465 reading EOG6QNN0J_1 244/465 reading EOG6PC9WN_1 245/465 reading EOG6Q8529_1 246/465 reading EOG6KSPP5_1 247/465 reading EOG6G1MMG_1 248/465 reading EOG63XV6Q_1 249/465 reading EOG6D531X_1 250/465 reading EOG61ZFF6_1 251/465 reading EOG6N5W22_1 252/465 reading EOG63V009_1 253/465 reading EOG6PK2CG_1 254/465 reading EOG6NP779_1 255/465 reading EOG6933N9_1 256/465 reading EOG68GW6V_1 257/465 reading EOG66Q6XP_1 258/465 reading EOG6JQ427_1 259/465 reading EOG6C5CNP_1 260/465 reading EOG6R5066_1 261/465 reading EOG6FTW4C_1 262/465 reading EOG6GXFRF_1 263/465 reading EOG65759X_1 264/465 reading EOG6KWJX8_1 265/465 reading EOG6QNN0N_1 266/465 reading EOG641QFN_1 267/465 reading EOG6S1TBT_1 268/465 reading EOG6GB79M_1 269/465 reading EOG65B1K2_1 270/465 reading EOG66WZD1_1 271/465 reading EOG65TCRK_1 272/465 reading EOG6PNXN7_1 273/465 reading EOG6FR0WR_1 274/465 reading EOG6QRH78_1 275/465 reading EOG6P2Q64_1 276/465 reading EOG666VQC_1 277/465 reading EOG6FJ8F2_1 278/465 reading EOG6HHP6H_1 279/465 reading EOG6DJK1Q_1 280/465 reading EOG63R3R5_1 281/465 reading EOG6PC9WF_1 282/465 reading EOG6Q58T0_1 283/465 reading EOG641QGH_1 284/465 reading EOG6933N7_1 285/465 reading EOG69S6BG_1 286/465 reading EOG64XJM7_1 287/465 reading EOG66Q6XR_1 288/465 reading EOG6PK2CM_1 289/465 reading EOG6NS3FV_1 290/465 reading EOG65MN9B_1 291/465 reading EOG641QFW_1 292/465 reading EOG63R3R9_1 293/465 reading EOG6DZ1ZZ_1 294/465 reading EOG6N04J6_1 295/465 reading EOG6CRM3G_1 296/465 reading EOG6GMV1P_1 297/465 reading EOG6S4PKX_1 298/465 reading EOG65MN9F_1 299/465 reading EOG6NP773_1 300/465 reading EOG6K6G7S_1 301/465 reading EOG6DZ201_1 302/465 reading EOG6BZN62_1 303/465 reading EOG68SGZ1_1 304/465 reading EOG69PB2Z_1 305/465 reading EOG6SXNGX_1 306/465 reading EOG6QZ7Q8_1 307/465 reading EOG6DR9GP_1 308/465 reading EOG6QFWJ6_1 309/465 reading EOG6QC18P_1 310/465 reading EOG6CG0CT_1 311/465 reading EOG6HHP6B_1 312/465 reading EOG6PK2CQ_1 313/465 reading EOG67D9KJ_1 314/465 reading EOG6JWVJQ_1 315/465 reading EOG6F1X6H_1 316/465 reading EOG6PG64S_1 317/465 reading EOG605S4Q_1 318/465 reading EOG6R7VF9_1 319/465 reading EOG6CZBM5_1 320/465 reading EOG6JT092_1 321/465 reading EOG6B5P96_1 322/465 reading EOG63R3RK_1 323/465 reading EOG64F6DK_1 324/465 reading EOG6FJ8D6_1 325/465 reading EOG6QZ7QX_1 326/465 reading EOG6F1X6M_1 327/465 reading EOG6001NN_1 328/465 reading EOG62V8KH_1 329/465 reading EOG695ZWC_1 330/465 reading EOG67PX9B_1 331/465 reading EOG6SBF2V_1 332/465 reading EOG6P8FNH_1 333/465 reading EOG6KSPQ0_1 334/465 reading EOG6GMV1H_1 335/465 reading EOG63R3RC_1 336/465 reading EOG6907D7_1 337/465 reading EOG6JWVHT_1 338/465 reading EOG68SGX8_1 339/465 reading EOG6HDSZ9_1 340/465 reading EOG6BK57S_1 341/465 reading EOG60K83N_1 342/465 reading EOG6SXNHD_1 343/465 reading EOG6KD6Q9_1 344/465 reading EOG68GW6Q_1 345/465 reading EOG6Q852G_1 346/465 reading EOG676K44_1 347/465 reading EOG6FN4NZ_1 348/465 reading EOG6Q58ST_1 349/465 reading EOG6933NR_1 350/465 reading EOG62JNVR_1 351/465 reading EOG64MXWZ_1 352/465 reading EOG6S1TC2_1 353/465 reading EOG6HT8WD_1 354/465 reading EOG63FH1F_1 355/465 reading EOG6PC9X3_1 356/465 reading EOG6Q58SW_1 357/465 reading EOG63N7HF_1 358/465 reading EOG6CRM3H_1 359/465 reading EOG6PRSVP_1 360/465 reading EOG6R5069_1 361/465 reading EOG6CC453_1 362/465 reading EOG6001PC_1 363/465 reading EOG63BMS7_1 364/465 reading EOG676K40_1 365/465 reading EOG64MXWK_1 366/465 reading EOG6N30SN_1 367/465 reading EOG6575BP_1 368/465 reading EOG67D9M5_1 369/465 reading EOG615GJK_1 370/465 reading EOG6RBQP0_1 371/465 reading EOG68KRFQ_1 372/465 reading EOG6DR9GZ_1 373/465 reading EOG6Q2DKD_1 374/465 reading EOG6255XM_1 375/465 reading EOG64BB5X_1 376/465 reading EOG6PG646_1 377/465 reading EOG62FSN7_1 378/465 reading EOG6H72G0_1 379/465 reading EOG6PZJB1_1 380/465 reading EOG64MXWG_1 381/465 reading EOG65QHHP_1 382/465 reading EOG6C87WM_1 383/465 reading EOG698V4R_1 384/465 reading EOG615GHV_1 385/465 reading EOG6FFD5G_1 386/465 reading EOG66WZCQ_1 387/465 reading EOG698V4H_1 388/465 reading EOG6NVZQ8_1 389/465 reading EOG6001NK_1 390/465 reading EOG6JDHB2_1 391/465 reading EOG62BXCX_1 392/465 reading EOG60K833_1 393/465 reading EOG62BXCZ_1 394/465 reading EOG6CG0D0_1 395/465 reading EOG6JM7SX_1 396/465 reading EOG69KFVF_1 397/465 reading EOG615GHP_1 398/465 reading EOG6KH2ZR_1 399/465 reading EOG683D8Q_1 400/465 reading EOG6PRSVM_1 401/465 reading EOG64J2NS_1 402/465 reading EOG66HGF5_1 403/465 reading EOG6DFPSF_1 404/465 reading EOG60P4BZ_1 405/465 reading EOG66MBPR_1 406/465 reading EOG6DFPSD_1 407/465 reading EOG67D9KC_1 408/465 reading EOG6HHP5S_1 409/465 reading EOG64BB5N_1 410/465 reading EOG6STS7W_1 411/465 reading EOG6DBTJX_1 412/465 reading EOG6FXRC9_1 413/465 reading EOG6DBTHZ_1 414/465 reading EOG6KH2ZD_1 415/465 reading EOG6STS87_1 416/465 reading EOG65TCS9_1 417/465 reading EOG67D9KV_1 418/465 reading EOG6SXNHG_1 419/465 reading EOG6255XS_1 420/465 reading EOG65MN8T_1 421/465 reading EOG6GF3JF_1 422/465 reading EOG66Q6X8_1 423/465 reading EOG6KSPPS_1 424/465 reading EOG61RPZ9_1 425/465 reading EOG637RJP_1 426/465 reading EOG66MBP7_1 427/465 reading EOG6J3WMR_1 428/465 reading EOG6B2T20_1 429/465 reading EOG6QJRRQ_1 430/465 reading EOG6GB79H_1 431/465 reading EOG6JDHBG_1 432/465 reading EOG6Q852B_1 433/465 reading EOG676K3Q_1 434/465 reading EOG6RV2WT_1 435/465 reading EOG6DV5QM_1 436/465 reading EOG6GTKHQ_1 437/465 reading EOG6FR0W5_1 438/465 reading EOG6NVZPZ_1 439/465 reading EOG6K0QRT_1 440/465 reading EOG65DWSM_1 441/465 reading EOG6CC452_1 442/465 reading EOG6G4GTX_1 443/465 reading EOG64BB5H_1 444/465 reading EOG64J2NC_1 445/465 reading EOG61G37F_1 446/465 reading EOG6H72G3_1 447/465 reading EOG6SBF2B_1 448/465 reading EOG695ZW1_1 449/465 reading EOG68WC58_1 450/465 reading EOG6CG0CX_1 451/465 reading EOG6FFD5V_1 452/465 reading EOG6G4GTT_1 453/465 reading EOG6K3M11_1 454/465 reading EOG651DTX_1 455/465 reading EOG60VVT3_1 456/465 reading EOG62NJ41_1 457/465 reading EOG66147J_1 458/465 reading EOG63FH1C_1 459/465 reading EOG6GXFR5_1 460/465 reading EOG61C70W_1 461/465 reading EOG6DV5QK_1 462/465 reading EOG6HQDPF_1 463/465 reading EOG6NVZPX_1 464/465 reading EOG6GXFR3_1 465/465 reading EOG6KPTG0_1
/home/amir/Dropbox/python_modules/reprophylo.py:1216: UserWarning: To get translations, add a feature manually
warnings.warn("To get translations, add a feature manually")
In [6]:
pickle_pj(pj, 'szitenberg_et_al_15_reprophylo')
Out[6]:
'szitenberg_et_al_15_reprophylo'
If the keyword project is False (default), the function returns a list of fasta file names and a list of Loci objects.
This is usefull when the loci are not all the same character type or feature type.
If project == False, the usage is:
filenames, loci_list = make_fasta_files_from_nexus(nexus_filename,
'data', 'dna', 'CDS')
pj = Project(loci_list)
for f in filenames:
locus_name = f.split('/')[-1].split('.')[0]
pj.read_alignment(f, 'dna','CDS',locus_name)
This takes a while (for both project=True and False) because a few things are happening at the background. It is worth while for downstream steps
Tip:¶
Next time you run, start here by unpickling the file:
pj = unpickle_pj('szitenberg_et_al_15_reprophylo')
This is much much faster than reading the data. Git will pick up with the same repository.
In [39]:
#pj = unpickle_pj('szitenberg_et_al_15_reprophylo')
2.2 Read a supplementary table with pandas¶
In [11]:
import pandas as pd
# This reads a supplementary table
# form Kawahara and Breinholt 2014
supp3 = 'data/Kawahara_Breinholt_2014/'+\
'rspb20140970supp3.csv'
metadata = pd.read_table(supp3, skiprows=2)
# This places the info from the table
# in the metadta of the sequence records:
# Iterate all the records (each sequence in each locus)
# and update their metadata based on the supplementary
# table
for r in pj.records:
source = r.features[0] # This is a Biopython (GenBank)
# source feature. Since we read a
# Nexus file, it was generated
# by ReproPhylo rather than read.
# If a GenBank file is read, the source
# and other features are read as well.
original_id = source.qualifiers['original_id'][0] # This is the nexus sequence header.
# To allow abstraction, the actual
# records id is generated by the system
# when formats other than GenBank or EMBL
# are read
record_metadata = metadata.loc[metadata['Sample ID'] == original_id] # The 'original_id' is the 'Sample ID'
# in the supplementary table.
# This will get the table line for
# the current 'original_id'.
record_metadata = record_metadata.to_dict() # This will turn the line into a dictionery
# with column names as keys.
# A dictionary is the python equivalent
# for the perl array.
for key in record_metadata: # This will add each value in the table
source.qualifiers[key] = [record_metadata[key].items()[0][1]] # line to the Biopython feature qualifiers
# in the source feature
source.qualifiers['organism'] = source.qualifiers['Taxa'] # the 'Taxa' column in the
# supplementary contains
# the 'organism' sensu GenBank
pickle_pj(pj, 'szitenberg_et_al_15_reprophylo')
/usr/local/lib/python2.7/dist-packages/pandas/io/excel.py:626: UserWarning: Installed openpyxl is not supported at this time. Use >=1.6.1 and <2.0.0. .format(openpyxl_compat.start_ver, openpyxl_compat.stop_ver))
Out[11]:
'szitenberg_et_al_15_reprophylo'
2.3 Manually assign species to clades¶
In [12]:
clades = {'Papilio glaucus': 'butterfilies', # This is a manual assignment of the 'organism'
'Macrosoma sp.*': 'butterfilies', # values to lepidopteran clades sensu
'Megathymus yuccae*': 'butterfilies', # Kawahara and Breinholt 2014.
'Semomesia campanea': 'butterfilies',
'Danaus plexippus*': 'butterfilies',
'Phyllocnistis citrella*': 'I',
'Plutella xylostella*': 'I',
'Grapholita dimorpha*': 'I',
'Lantanophaga pusillidactyla*': 'I',
'Urodus parvula*': 'I',
'Morpheis mathani*': 'I',
'Megalopyge tharops*': 'I',
'Dalcera abrasa*': 'I',
'Thubana sp.*': 'III',
'Pterodecta felderi*': 'III',
'Zeuzerodes maculata*': 'III',
'Lacosoma ludolpha*': 'IV',
'Lyssa zampa*': 'IV',
'Nothus lunus*': 'IV',
'Nemoria lixaria*': 'IV',
'Anigraea sp.': 'IV',
'Bombyx mori*': 'IV',
'Manduca sexta*': 'IV',
'Artace sp.*': 'IV',
'Myelobia sp.*': 'IV',
'Actias luna*': 'IV'}
pj.add_qualifier_from_source('Taxa') # This copies the 'Taxa' qualifier from the source
# feature to all the other features in the record
# (Biopython SeqFeature. See detailed explanation
# in the ReproPhylo manual). It is not necessary,
# but good practice, because we might want to edit
# it for non-source features and keep the original
# as backup in the source feature.
for taxon in clades: # This will assign a 'Clade' qualifier to each
pj.if_this_then_that(taxon, 'Taxa', clades[taxon], 'Clade') # feature in each record based on the 'clades'
# dictionary, manually created above.
# If we were doing this in a project that contains trees,
# the following line makes sure the trees
# are informed of the changes to the metadata:
pj.propagate_metadata()
2.4 Export all the records to a text file¶
A text file is not required for downstream process, but can be written for insepction. The default format is GenBank. Other complete representations of the data are the EMBL and CSV formats. All other formats can be chosen as well, but they will not represent the metadta.
In [13]:
pj.write('data/sequence_and_metadata.gb') # GenBank
pj.write('data/sequence_and_metadata.csv', format='csv') # spreadsheet
Example GenBank formated record¶
LOCUS denovo0 1357 bp DNA UNK 01-JAN-1980
DEFINITION .
ACCESSION denovo0
VERSION denovo0
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers # These are annotations and not a part of the output
source 1..1357 # ==================================================
/Sample ID="Bmoricds" # From the supplementary table
/Minimum contig size=87 # From the supplementary table
/Superfamily="Bombycoidea" # From the supplementary table
/Family="Bombycidae" # From the supplementary table
/#taxa Per lane="nan" # From the supplementary table
/Locality="nan" # From the supplementary table
/Taxa="Bombyx mori" # From the supplementary table
/Collector="nan" # From the supplementary table
/Genbank SRA accession number="nan" # From the supplementary table
/Maximum contig size=56289 # From the supplementary table
/N50=1698 # From the supplementary table
/Collection date="nan" # From the supplementary table
/feature_id="denovo0_source" # SYSTEM GENERATED
/Collection country/region="nan" # From the supplementary table
/original_id="Bmoricds" # NEXUS FILE SEQUENCE HEADER
/original_desc # Only when fasta or stockholm are read
/# of contigs=14623 # From the supplementary table
/Mean contig size=1224 # From the supplementary table
/Total bp=17891307 # From the supplementary table
/Data type="Genomic gene set" # From the supplementary table
/organism="Bombyx mori" # CREATED ABOVE
CDS 1..1357 #
/Taxa="Bombyx mori" # CREATED ABOVE
/Clade="IV" # CREATED ABOVE
/nuc_degen_prop="0.0707442888725" # SYSTEM GENERATED
/feature_id="denovo0_f0" # SYSTEM GENERATED
/GC_content="43.0361090641" # SYSTEM GENERATED
/gene="EOG69CQC1_1" # THE SET NAME FROM THE CHARSET COMMAND IN THE NEXUS FILE
ORIGIN
1 cagtgcaagg gtattaytaa ggccgacagt gtccgcgaag taacacgcat ccggtgcagt
61 aaytmgatgc ccmgg[...] # Truncated for presentation
//
2.5 Making sure all-gap positions are removed from the read alignments¶
There is no sequence alignment step in this analysis because we read aligned sequences. To learn about sequene alignmnet with MAFFT or MUSCLE in ReproPhylo, see the case studies in the manual. The syntax is similar to that of the trimming step which will be done next.
Alignmnet trimming is done with TrimAl, which allows automated heuristic approaches or manual approaches. Here we use it only to remove all gaps positions because we want to keep the alignmnet as it was used in the original publication. See the manual for more options.
In [14]:
# make a TrimAl configuration object
trimal = TrimalConf(pj, # The Project instance
method_name='no_trim', # Any unique string
trimal_commands={'noallgaps': True}) # Any TrimAl command line argument
# TrimAl Flags receive True or False
# Every Conf object gets a unique generated ID, even
# if the method name was used in this Project.
# If an existing method name
# is reused, its results will be overwritten, and
# it will be distinguised from previous versions by
# the system ID.
trimal -in 861921429737580.9_EOG6PRSVJ_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6FJ8F2_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG65MN9F_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6Q852B_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG66Q6XR_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6PRSVM_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG64MXWK_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG60K83N_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6933NR_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6QRH81_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6K6G7Z_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6R5069_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6STS8H_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG698V4R_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG64TPCQ_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG63BMS7_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG68GW77_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6BZN62_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6QZ7QX_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6GTKHJ_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6HHP5S_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6GB79H_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG68KRG8_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6MKNM3_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6FXRCN_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6K0QSG_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG63FH1T_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6DJK1Q_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG698V4H_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6JWVHT_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG65X80D_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG61JZGH_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG60VVST_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6QRH78_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6PZJB1_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6NS3G8_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG65TCRN_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG63R3RC_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6C87X4_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG64TPC4_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG64MXWG_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG61G385_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6NVZQ8_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6N04JN_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG67SSJJ_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG62NJ41_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG68GW71_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6Q58ST_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6FXRCK_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6PVP2X_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG676K3Q_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6DBTK0_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6KH2ZR_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG66HGF2_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG64MXX7_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6F1X6H_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG66147D_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6FFD5V_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6RXZ3G_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6C5CPH_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6PC9WG_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6DNF7N_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6GHZSR_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6M65N6_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG62V8KH_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6DNF8K_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6QVCGS_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG69GKKW_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6FFD5G_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG64J2NC_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6R5066_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG66WZD1_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6GHZSZ_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG69CQBW_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG63JC90_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG634W9M_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6255XM_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6BK57S_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG68WC5N_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG68D104_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG65B1K2_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6SXNH7_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG63JC8S_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6KH2ZX_1@ReadDirectly.fasta -noallgaps trimal -in 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861921429737580.9_EOG6K9BGH_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG67D9KJ_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6BCDR6_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6GTKHQ_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6FN4N0_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6JDHBD_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG615GHV_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6CJVMH_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6CC44S_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6B2T20_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6JQ41Z_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG637RJP_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6QRH88_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6933N9_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG605S4Z_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6J3WMR_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6Q58T0_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6BVRZ3_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6CJVMM_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6Q8524_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6PNXN7_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6QFWHZ_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6SXNHD_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6B5P96_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6C87WM_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG63212K_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG63XV6Q_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG66Q6XP_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6Q852G_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG66MBPR_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6RNBCT_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG67WNS9_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6HQDPF_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG66Q6X8_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG63R3QZ_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6B8JHP_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6HT8WD_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG641QGH_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG669QZR_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6GMV1P_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG61RPZ9_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG66147J_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG60K843_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6BG90S_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG602WX4_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6GF3JF_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6PC9X3_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6HQDPG_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG64QT4T_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6BG909_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6H4677_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG69ZXTF_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6NVZPX_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG68KRFQ_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG60P4BJ_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6P8FNH_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6N8R81_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG60VVTG_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6RJG4W_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6JT09B_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG670TNG_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6CG0CX_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6D26TV_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG666VQ4_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6FTW4C_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG60VVT3_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG64BB5X_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG654930_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6Q2DJZ_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG63R3R5_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6QFWJH_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6SN1SH_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6894QQ_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6HX54P_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6QFWJ6_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6FJ8D6_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6R7VF9_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6S4PKX_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG680J16_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6PK2CG_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6H72G0_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6PNXM9_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG67PX9B_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG64F6DH_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG65759X_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6PG646_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6KKZ71_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6JM7SX_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6DZ201_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6SBF2V_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG65MN8T_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6NP773_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG68SGX8_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6J3WM7_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6STS87_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG651DV5_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG66DM62_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG605S4X_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6K3M19_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6NZTXP_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG65493R_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG69GKMS_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG60ZR1Z_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6D5327_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6PNXM6_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6575BP_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG68D102_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG60ZR1T_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6GXFR5_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6NS3FV_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG62V8KS_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6PRSVP_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6JWVJQ_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6QZ7Q8_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6NVZPZ_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG63N7HX_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6QC198_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6C2HF4_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6NP779_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6S1TBX_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6F7NPN_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6D26TG_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6CJVMQ_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG63BMSG_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6QZ7R6_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6SXNHG_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG69S6BG_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6R506X_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG608ND4_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6640GX_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6G4GTT_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG695ZWC_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6S1TC2_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG69KFVF_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG683D8Q_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG66MBNX_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG680J15_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6GMV1H_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG69KFV8_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG66WZCQ_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6KSPPS_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6PRSVH_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG615GJK_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG68SGXD_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6P2Q5K_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG67D9KC_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6SJ5JS_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6B8JHC_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG61RPZF_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6P8FNB_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6J6RV9_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6SJ5K0_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG65X811_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG63V009_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6DZ1ZZ_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6KWJXS_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6KKZ6X_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6S1TBT_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6FR0W5_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6SQX12_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6M39DN_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6CC44M_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6FFD5C_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG63R3RK_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG65TCRS_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6C87X0_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6RFKXS_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG6R506Q_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG676K44_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG64MXWZ_1@ReadDirectly.fasta -noallgaps trimal -in 861921429737580.9_EOG68WC5K_1@ReadDirectly.fasta -noallgaps
The TrimalConf default values:¶
TrimalConf(pj,
method_name='gappyout',
program_name='trimal',
cmd='default', # The defaults cmd is in Project.defaults['trimal']
# You can change the default value or provide it here.
alns='all', # Or a list of specific alignmnet names.
trimal_commands={'gappyout': True})
Trimming execution¶
The trim Project method excepts a list of one or more TrimalConf objects. Different objects can be used to trim different subsets of alignments.
In [15]:
pj.trim([trimal])
2.6 Preparing supermatrices from 200 loci long sliding windows along the entropy gradient¶
2.6.1 Calculating the statistics¶
Entropy, conservation, and gap score will be calculated for each position in each alignmnet.
Sequence length and GC content will be calculated for each untrimmed sequence in each locus.
This is done by passing the Project instance (pj) into a LociStats object:
In [4]:
stats = LociStats(pj, # The Project instance
trimmed=True, # Only trimmed alignments will be checked
alignmnet_method=None, # If specified, only regard alignments created
# with this method
trimming_method=None) # If specified, only regard alignments trimmed
# with this method
# By default, only regard the first occurance
# of each locus, if it was aligned or trimmed
# using more than one method
2.6.2 Sort the alignmnets according to statistics values¶
This done by using the sort method of the LociStats instance:
In [5]:
stats.sort(parameter = 'entropy', # Sort the loci according to entropy values
percentile=50, # First sort by the specified percentile of each locus,
# typically, the median
percentile_range=(25,75), # Then, sort by the distance between the specified percentiles
# for each locus, typically the 25 and 75 percentiles
reverse = True) # Sort in descending order
2.6.3 Figure 2 A¶
The next cell produced Figure 2A. It plots the entropy distribution as a box-plot for each locus. The brown dot is the median, the blue stretch is the 25-75 percentiles, the black stretches are the > 95 and < 5 percentiles.
In [6]:
%matplotlib inline
stats.plot('entropy.png', # Output file name
figsize=(30,7), # Figure size in cm
params=['entropy'],# The parameters to include.
# can take a list of just one or a few parameters
# including 'entropy','conservation', 'gapscore'
# 'sequence_length' and 'sequence_gc'
lable_fsize=40,
xtick_fsize=0,
ytick_fsize=1,
boxcolor='DodgerBlue',
whiskercolor='black',
capcolor='black',
mediancolor='SaddleBrown',
medianline_w=5)
2.6.4 Figure S1, Plot a box plot for each parameter for each locus¶
In the resulting figure the loci will be sorted in a descending order of the entropy median, as a result of the above sorting step. As expected, entropy is correlated with the conservation value. It is not correlated with other measures which makes its effect easy to check.
In [5]:
stats.plot('plot.png', # Output file name
figsize=(50,23), # Figure size in cm
params='all', # The parameters to include.
# can take a list of just one
# or a few parameters
# including 'entropy','conservation',
# 'gapscore', 'sequence_length'
# and 'sequence_gc'
lable_fsize=20,
xtick_fsize=10,
ytick_fsize=1,
boxcolor='salmon',
whiskercolor='gray',
capcolor='black',
mediancolor='white',
medianline_w=3)
2.7 Prepare the Concatenation objects¶
Concatenation objects contain the configuration information for building a supermatrix. This will produce six Concatenation objects each with a sliding window of 200 loci, along the entropy gradient.
In [21]:
concatenations = stats.slide_loci('source_original_id', # OTU metadata value.
# sequences from different loci
# ,which share this value,
# will be considered to belong to
# the same sample and will be
# concatenated
median_range='all', # Before starting the slide,
# you can exclude loci
parameter='entropy', # which median fall outside
# the specified range
# of the specified parameter.
# The remaining loci will still
# be sorted according to the
# parameter specified in the
# sorting step above, and not
# according to the parameter that
# specified here, if it is
# different from above.
start=0, # Counting from the first locus
# that was not excluded,
# start the first window here.
length=200, # the length of the window,
# counting 200 loci that were
# not filtered out
step=50) # the length of the slide.
# Add the concatenation objects to the project
for concat in concatenations:
pj.add_concatenation(concat)
# Create the supermatrices
pj.make_concatenation_alignments()
# And collect their names
aln_names = [c.name for c in pj.concatenations]
entropy_1.14_0.00_loci_0_to_199 entropy_0.48_0.00_loci_50_to_249 entropy_0.30_0.00_loci_100_to_299 entropy_0.00_0.00_loci_150_to_349 entropy_0.00_0.00_loci_200_to_399 entropy_0.00_0.00_loci_250_to_449 Concatenation entropy_1.14_0.00_loci_0_to_199 will have the following data OTU EOG6M65NR_1 EOG6SN1SH_1 EOG654933_1 EOG66147B_1 EOG680J15_1 EOG6S7JTK_1 EOG60ZR1Z_1 EOG6DBTJG_1 EOG69ZXTF_1 EOG64QT4T_1 EOG6K3M19_1 EOG60P4BJ_1 EOG6DBTK0_1 EOG64MXX7_1 EOG6GTKHJ_1 EOG6NVZQC_1 EOG6MPHV2_1 EOG68KRFS_1 EOG6GHZSR_1 EOG666VQ4_1 EOG651DV5_1 EOG6JDHBD_1 EOG63212K_1 EOG68D102_1 EOG6CJVMH_1 EOG60VVTB_1 EOG698V46_1 EOG6N8R81_1 EOG6FXRCK_1 EOG6R2400_1 EOG68KRG4_1 EOG61C70T_1 EOG6SJ5JS_1 EOG63212W_1 EOG6F7NPJ_1 EOG695ZW4_1 EOG61NTQM_1 EOG6NZTZ3_1 EOG6J3WM7_1 EOG68SGXM_1 EOG6RNBCT_1 EOG6M39DN_1 EOG6RFKXS_1 EOG6RXZ4G_1 EOG67SSJJ_1 EOG69GKKW_1 EOG6NZTXP_1 EOG6QFWHZ_1 EOG68PMPX_1 EOG6RFKXB_1 EOG62BXD6_1 EOG647FXX_1 EOG6B8JHP_1 EOG6S1TBX_1 EOG6DFPRT_1 EOG65HS25_1 EOG6FFD5C_1 EOG6R506D_1 EOG670TNG_1 EOG6F4SFZ_1 EOG6QVCGP_1 EOG65TCRS_1 EOG6QRH88_1 EOG6M65N6_1 EOG61G385_1 EOG6QRH81_1 EOG6RJG4W_1 EOG6K0QSG_1 EOG6KKZ6X_1 EOG60VVTG_1 EOG6D26TG_1 EOG6QZ7R6_1 EOG679FBS_1 EOG61RPZF_1 EOG6PC9WG_1 EOG60GCVD_1 EOG6R506Q_1 EOG605S4X_1 EOG65TCRN_1 EOG608ND4_1 EOG6640GX_1 EOG6SQX12_1 EOG69GKMS_1 EOG6D26TV_1 EOG605S4Z_1 EOG6N04JN_1 EOG67WNS9_1 EOG64TPCQ_1 EOG6NS3GS_1 EOG6NP76T_1 EOG63JC90_1 EOG67H5V2_1 EOG6NP77P_1 EOG6QFWJH_1 EOG6N04K4_1 EOG6CJVMQ_1 EOG6DZ204_1 EOG6C5CPH_1 EOG6FFD51_1 EOG6NP779_1 EOG6933N9_1 EOG6JQ427_1 EOG6C5CNP_1 EOG6FTW4C_1 EOG65759X_1 EOG6QNN0N_1 EOG66WZD1_1 EOG6FR0WR_1 EOG6P2Q64_1 EOG666VQC_1 EOG63R3R5_1 EOG641QGH_1 EOG69S6BG_1 EOG64XJM7_1 EOG65MN9B_1 EOG641QFW_1 EOG63R3R9_1 EOG6N04J6_1 EOG6GMV1P_1 EOG6S4PKX_1 EOG6NP773_1 EOG6DZ201_1 EOG6QFWJ6_1 EOG6CG0CT_1 EOG6HHP6B_1 EOG605S4Q_1 EOG6R7VF9_1 EOG6CZBM5_1 EOG6JT092_1 EOG6FJ8D6_1 EOG6QZ7QX_1 EOG6F1X6M_1 EOG6SBF2V_1 EOG6KSPQ0_1 EOG6GMV1H_1 EOG63R3RC_1 EOG68SGX8_1 EOG6BK57S_1 EOG60K83N_1 EOG6KD6Q9_1 EOG68GW6Q_1 EOG6Q852G_1 EOG676K44_1 EOG6FN4NZ_1 EOG6S1TC2_1 EOG6HT8WD_1 EOG63FH1F_1 EOG6PRSVP_1 EOG6R5069_1 EOG6CC453_1 EOG6001PC_1 EOG676K40_1 EOG6N30SN_1 EOG67D9M5_1 EOG6RBQP0_1 EOG6Q2DKD_1 EOG6255XM_1 EOG64BB5X_1 EOG6H72G0_1 EOG6PZJB1_1 EOG64MXWG_1 EOG65QHHP_1 EOG698V4R_1 EOG615GHV_1 EOG6FFD5G_1 EOG6NVZQ8_1 EOG60K833_1 EOG62BXCZ_1 EOG6CG0D0_1 EOG69KFVF_1 EOG615GHP_1 EOG683D8Q_1 EOG6PRSVM_1 EOG64J2NS_1 EOG66HGF5_1 EOG60P4BZ_1 EOG66MBPR_1 EOG6DFPSD_1 EOG64BB5N_1 EOG6DBTJX_1 EOG6FXRC9_1 EOG6STS87_1 EOG6SXNHG_1 EOG6255XS_1 EOG6GF3JF_1 EOG6KSPPS_1 EOG637RJP_1 EOG6J3WMR_1 EOG6B2T20_1 EOG6GB79H_1 EOG6JDHBG_1 EOG676K3Q_1 EOG6RV2WT_1 EOG6GTKHQ_1 EOG6FR0W5_1 EOG6CC452_1 EOG61G37F_1 EOG6GXFR5_1 EOG6DV5QK_1 EOG6KPTG0_1 Dplexcds denovo28_f0 denovo80_f0 denovo106_f0 denovo132_f0 denovo210_f0 denovo236_f0 denovo262_f0 denovo288_f0 denovo340_f0 denovo418_f0 denovo522_f0 denovo574_f0 denovo600_f0 denovo730_f0 denovo782_f0 denovo938_f0 denovo964_f0 denovo1042_f0 denovo1068_f0 denovo1146_f0 denovo1302_f0 denovo1484_f0 denovo1510_f0 denovo1640_f0 denovo1744_f0 denovo1770_f0 denovo1796_f0 denovo1952_f0 denovo2134_f0 denovo2186_f0 denovo2238_f0 denovo2264_f0 denovo2342_f0 denovo2446_f0 denovo2472_f0 denovo2498_f0 denovo2524_f0 denovo2576_f0 denovo2602_f0 denovo2654_f0 denovo2758_f0 denovo2784_f0 denovo2836_f0 denovo2862_f0 denovo2914_f0 denovo2992_f0 denovo3044_f0 denovo3148_f0 denovo3226_f0 denovo3252_f0 denovo3278_f0 denovo3304_f0 denovo3330_f0 denovo3434_f0 denovo3486_f0 denovo3590_f0 denovo3616_f0 denovo3668_f0 denovo3694_f0 denovo3720_f0 denovo3772_f0 denovo3850_f0 denovo3954_f0 denovo3980_f0 denovo4032_f0 denovo4058_f0 denovo4188_f0 denovo4292_f0 denovo4318_f0 denovo4344_f0 denovo4396_f0 denovo4448_f0 denovo4552_f0 denovo4630_f0 denovo4734_f0 denovo4760_f0 denovo4786_f0 denovo4838_f0 denovo4890_f0 denovo4916_f0 denovo4942_f0 denovo4968_f0 denovo4994_f0 denovo5202_f0 denovo5228_f0 denovo5254_f0 denovo5384_f0 denovo5436_f0 denovo5514_f0 denovo5592_f0 denovo5618_f0 denovo5644_f0 denovo5930_f0 denovo6008_f0 denovo6060_f0 denovo6112_f0 denovo6216_f0 denovo6242_f0 denovo6268_f0 denovo6580_f0 denovo6606_f0 denovo6684_f0 denovo6710_f0 denovo6762_f0 denovo6814_f0 denovo6866_f0 denovo6996_f0 denovo7074_f0 denovo7126_f0 denovo7152_f0 denovo7256_f0 denovo7334_f0 denovo7386_f0 denovo7412_f0 denovo7516_f0 denovo7542_f0 denovo7568_f0 denovo7620_f0 denovo7672_f0 denovo7698_f0 denovo7750_f0 denovo7802_f0 denovo7984_f0 denovo8036_f0 denovo8062_f0 denovo8218_f0 denovo8244_f0 denovo8270_f0 denovo8296_f0 denovo8400_f0 denovo8426_f0 denovo8452_f0 denovo8582_f0 denovo8634_f0 denovo8660_f0 denovo8686_f0 denovo8764_f0 denovo8816_f0 denovo8842_f0 denovo8894_f0 denovo8920_f0 denovo8946_f0 denovo8972_f0 denovo8998_f0 denovo9128_f0 denovo9154_f0 denovo9180_f0 denovo9310_f0 denovo9336_f0 denovo9362_f0 denovo9388_f0 denovo9440_f0 denovo9492_f0 denovo9544_f0 denovo9596_f0 denovo9674_f0 denovo9700_f0 denovo9726_f0 denovo9804_f0 denovo9830_f0 denovo9856_f0 denovo9882_f0 denovo9934_f0 denovo9960_f0 denovo9986_f0 denovo10064_f0 denovo10168_f0 denovo10194_f0 denovo10220_f0 denovo10272_f0 denovo10298_f0 denovo10350_f0 denovo10376_f0 denovo10402_f0 denovo10428_f0 denovo10480_f0 denovo10506_f0 denovo10532_f0 denovo10610_f0 denovo10662_f0 denovo10688_f0 denovo10766_f0 denovo10844_f0 denovo10870_f0 denovo10922_f0 denovo10974_f0 denovo11026_f0 denovo11078_f0 denovo11104_f0 denovo11156_f0 denovo11182_f0 denovo11234_f0 denovo11260_f0 denovo11312_f0 denovo11338_f0 denovo11442_f0 denovo11546_f0 denovo11910_f0 denovo11962_f0 denovo12066_f0 FG120077 denovo36_f0 denovo88_f0 denovo114_f0 denovo140_f0 denovo218_f0 denovo244_f0 denovo270_f0 denovo296_f0 denovo348_f0 denovo426_f0 denovo530_f0 denovo582_f0 denovo608_f0 denovo738_f0 denovo790_f0 denovo946_f0 denovo972_f0 denovo1050_f0 denovo1076_f0 denovo1154_f0 denovo1310_f0 denovo1492_f0 denovo1518_f0 denovo1648_f0 denovo1752_f0 denovo1778_f0 denovo1804_f0 denovo1960_f0 denovo2142_f0 denovo2194_f0 denovo2246_f0 denovo2272_f0 denovo2350_f0 denovo2454_f0 denovo2480_f0 denovo2506_f0 denovo2532_f0 denovo2584_f0 denovo2610_f0 denovo2662_f0 denovo2766_f0 denovo2792_f0 denovo2844_f0 denovo2870_f0 denovo2922_f0 denovo3000_f0 denovo3052_f0 denovo3156_f0 denovo3234_f0 denovo3260_f0 denovo3286_f0 denovo3312_f0 denovo3338_f0 denovo3442_f0 denovo3494_f0 denovo3598_f0 denovo3624_f0 denovo3676_f0 denovo3702_f0 denovo3728_f0 denovo3780_f0 denovo3858_f0 denovo3962_f0 denovo3988_f0 denovo4040_f0 denovo4066_f0 denovo4196_f0 denovo4300_f0 denovo4326_f0 denovo4352_f0 denovo4404_f0 denovo4456_f0 denovo4560_f0 denovo4638_f0 denovo4742_f0 denovo4768_f0 denovo4794_f0 denovo4846_f0 denovo4898_f0 denovo4924_f0 denovo4950_f0 denovo4976_f0 denovo5002_f0 denovo5210_f0 denovo5236_f0 denovo5262_f0 denovo5392_f0 denovo5444_f0 denovo5522_f0 denovo5600_f0 denovo5626_f0 denovo5652_f0 denovo5938_f0 denovo6016_f0 denovo6068_f0 denovo6120_f0 denovo6224_f0 denovo6250_f0 denovo6276_f0 denovo6588_f0 denovo6614_f0 denovo6692_f0 denovo6718_f0 denovo6770_f0 denovo6822_f0 denovo6874_f0 denovo7004_f0 denovo7082_f0 denovo7134_f0 denovo7160_f0 denovo7264_f0 denovo7342_f0 denovo7394_f0 denovo7420_f0 denovo7524_f0 denovo7550_f0 denovo7576_f0 denovo7628_f0 denovo7680_f0 denovo7706_f0 denovo7758_f0 denovo7810_f0 denovo7992_f0 denovo8044_f0 denovo8070_f0 denovo8226_f0 denovo8252_f0 denovo8278_f0 denovo8304_f0 denovo8408_f0 denovo8434_f0 denovo8460_f0 denovo8590_f0 denovo8642_f0 denovo8668_f0 denovo8694_f0 denovo8772_f0 denovo8824_f0 denovo8850_f0 denovo8902_f0 denovo8928_f0 denovo8954_f0 denovo8980_f0 denovo9006_f0 denovo9136_f0 denovo9162_f0 denovo9188_f0 denovo9318_f0 denovo9344_f0 denovo9370_f0 denovo9396_f0 denovo9448_f0 denovo9500_f0 denovo9552_f0 denovo9604_f0 denovo9682_f0 denovo9708_f0 denovo9734_f0 denovo9812_f0 denovo9838_f0 denovo9864_f0 denovo9890_f0 denovo9942_f0 denovo9968_f0 denovo9994_f0 denovo10072_f0 denovo10176_f0 denovo10202_f0 denovo10228_f0 denovo10280_f0 denovo10306_f0 denovo10358_f0 denovo10384_f0 denovo10410_f0 denovo10436_f0 denovo10488_f0 denovo10514_f0 denovo10540_f0 denovo10618_f0 denovo10670_f0 denovo10696_f0 denovo10774_f0 denovo10852_f0 denovo10878_f0 denovo10930_f0 denovo10982_f0 denovo11034_f0 denovo11086_f0 denovo11112_f0 denovo11164_f0 denovo11190_f0 denovo11242_f0 denovo11268_f0 denovo11320_f0 denovo11346_f0 denovo11450_f0 denovo11554_f0 denovo11918_f0 denovo11970_f0 denovo12074_f0 SRR803483 denovo46_f0 denovo98_f0 denovo124_f0 denovo150_f0 denovo228_f0 denovo254_f0 denovo280_f0 denovo306_f0 denovo358_f0 denovo436_f0 denovo540_f0 denovo592_f0 denovo618_f0 denovo748_f0 denovo800_f0 denovo956_f0 denovo982_f0 denovo1060_f0 denovo1086_f0 denovo1164_f0 denovo1320_f0 denovo1502_f0 denovo1528_f0 denovo1658_f0 denovo1762_f0 denovo1788_f0 denovo1814_f0 denovo1970_f0 denovo2152_f0 denovo2204_f0 denovo2256_f0 denovo2282_f0 denovo2360_f0 denovo2464_f0 denovo2490_f0 denovo2516_f0 denovo2542_f0 denovo2594_f0 denovo2620_f0 denovo2672_f0 denovo2776_f0 denovo2802_f0 denovo2854_f0 denovo2880_f0 denovo2932_f0 denovo3010_f0 denovo3062_f0 denovo3166_f0 denovo3244_f0 denovo3270_f0 denovo3296_f0 denovo3322_f0 denovo3348_f0 denovo3452_f0 denovo3504_f0 denovo3608_f0 denovo3634_f0 denovo3686_f0 denovo3712_f0 denovo3738_f0 denovo3790_f0 denovo3868_f0 denovo3972_f0 denovo3998_f0 denovo4050_f0 denovo4076_f0 denovo4206_f0 denovo4310_f0 denovo4336_f0 denovo4362_f0 denovo4414_f0 denovo4466_f0 denovo4570_f0 denovo4648_f0 denovo4752_f0 denovo4778_f0 denovo4804_f0 denovo4856_f0 denovo4908_f0 denovo4934_f0 denovo4960_f0 denovo4986_f0 denovo5012_f0 denovo5220_f0 denovo5246_f0 denovo5272_f0 denovo5402_f0 denovo5454_f0 denovo5532_f0 denovo5610_f0 denovo5636_f0 denovo5662_f0 denovo5948_f0 denovo6026_f0 denovo6078_f0 denovo6130_f0 denovo6234_f0 denovo6260_f0 denovo6286_f0 denovo6598_f0 denovo6624_f0 denovo6702_f0 denovo6728_f0 denovo6780_f0 denovo6832_f0 denovo6884_f0 denovo7014_f0 denovo7092_f0 denovo7144_f0 denovo7170_f0 denovo7274_f0 denovo7352_f0 denovo7404_f0 denovo7430_f0 denovo7534_f0 denovo7560_f0 denovo7586_f0 denovo7638_f0 denovo7690_f0 denovo7716_f0 denovo7768_f0 denovo7820_f0 denovo8002_f0 denovo8054_f0 denovo8080_f0 denovo8236_f0 denovo8262_f0 denovo8288_f0 denovo8314_f0 denovo8418_f0 denovo8444_f0 denovo8470_f0 denovo8600_f0 denovo8652_f0 denovo8678_f0 denovo8704_f0 denovo8782_f0 denovo8834_f0 denovo8860_f0 denovo8912_f0 denovo8938_f0 denovo8964_f0 denovo8990_f0 denovo9016_f0 denovo9146_f0 denovo9172_f0 denovo9198_f0 denovo9328_f0 denovo9354_f0 denovo9380_f0 denovo9406_f0 denovo9458_f0 denovo9510_f0 denovo9562_f0 denovo9614_f0 denovo9692_f0 denovo9718_f0 denovo9744_f0 denovo9822_f0 denovo9848_f0 denovo9874_f0 denovo9900_f0 denovo9952_f0 denovo9978_f0 denovo10004_f0 denovo10082_f0 denovo10186_f0 denovo10212_f0 denovo10238_f0 denovo10290_f0 denovo10316_f0 denovo10368_f0 denovo10394_f0 denovo10420_f0 denovo10446_f0 denovo10498_f0 denovo10524_f0 denovo10550_f0 denovo10628_f0 denovo10680_f0 denovo10706_f0 denovo10784_f0 denovo10862_f0 denovo10888_f0 denovo10940_f0 denovo10992_f0 denovo11044_f0 denovo11096_f0 denovo11122_f0 denovo11174_f0 denovo11200_f0 denovo11252_f0 denovo11278_f0 denovo11330_f0 denovo11356_f0 denovo11460_f0 denovo11564_f0 denovo11928_f0 denovo11980_f0 denovo12084_f0 FG120035 denovo31_f0 denovo83_f0 denovo109_f0 denovo135_f0 denovo213_f0 denovo239_f0 denovo265_f0 denovo291_f0 denovo343_f0 denovo421_f0 denovo525_f0 denovo577_f0 denovo603_f0 denovo733_f0 denovo785_f0 denovo941_f0 denovo967_f0 denovo1045_f0 denovo1071_f0 denovo1149_f0 denovo1305_f0 denovo1487_f0 denovo1513_f0 denovo1643_f0 denovo1747_f0 denovo1773_f0 denovo1799_f0 denovo1955_f0 denovo2137_f0 denovo2189_f0 denovo2241_f0 denovo2267_f0 denovo2345_f0 denovo2449_f0 denovo2475_f0 denovo2501_f0 denovo2527_f0 denovo2579_f0 denovo2605_f0 denovo2657_f0 denovo2761_f0 denovo2787_f0 denovo2839_f0 denovo2865_f0 denovo2917_f0 denovo2995_f0 denovo3047_f0 denovo3151_f0 denovo3229_f0 denovo3255_f0 denovo3281_f0 denovo3307_f0 denovo3333_f0 denovo3437_f0 denovo3489_f0 denovo3593_f0 denovo3619_f0 denovo3671_f0 denovo3697_f0 denovo3723_f0 denovo3775_f0 denovo3853_f0 denovo3957_f0 denovo3983_f0 denovo4035_f0 denovo4061_f0 denovo4191_f0 denovo4295_f0 denovo4321_f0 denovo4347_f0 denovo4399_f0 denovo4451_f0 denovo4555_f0 denovo4633_f0 denovo4737_f0 denovo4763_f0 denovo4789_f0 denovo4841_f0 denovo4893_f0 denovo4919_f0 denovo4945_f0 denovo4971_f0 denovo4997_f0 denovo5205_f0 denovo5231_f0 denovo5257_f0 denovo5387_f0 denovo5439_f0 denovo5517_f0 denovo5595_f0 denovo5621_f0 denovo5647_f0 denovo5933_f0 denovo6011_f0 denovo6063_f0 denovo6115_f0 denovo6219_f0 denovo6245_f0 denovo6271_f0 denovo6583_f0 denovo6609_f0 denovo6687_f0 denovo6713_f0 denovo6765_f0 denovo6817_f0 denovo6869_f0 denovo6999_f0 denovo7077_f0 denovo7129_f0 denovo7155_f0 denovo7259_f0 denovo7337_f0 denovo7389_f0 denovo7415_f0 denovo7519_f0 denovo7545_f0 denovo7571_f0 denovo7623_f0 denovo7675_f0 denovo7701_f0 denovo7753_f0 denovo7805_f0 denovo7987_f0 denovo8039_f0 denovo8065_f0 denovo8221_f0 denovo8247_f0 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denovo286_f0 denovo338_f0 denovo416_f0 denovo520_f0 denovo572_f0 denovo598_f0 denovo728_f0 denovo780_f0 denovo936_f0 denovo962_f0 denovo1040_f0 denovo1066_f0 denovo1144_f0 denovo1300_f0 denovo1482_f0 denovo1508_f0 denovo1638_f0 denovo1742_f0 denovo1768_f0 denovo1794_f0 denovo1950_f0 denovo2132_f0 denovo2184_f0 denovo2236_f0 denovo2262_f0 denovo2340_f0 denovo2444_f0 denovo2470_f0 denovo2496_f0 denovo2522_f0 denovo2574_f0 denovo2600_f0 denovo2652_f0 denovo2756_f0 denovo2782_f0 denovo2834_f0 denovo2860_f0 denovo2912_f0 denovo2990_f0 denovo3042_f0 denovo3146_f0 denovo3224_f0 denovo3250_f0 denovo3276_f0 denovo3302_f0 denovo3328_f0 denovo3432_f0 denovo3484_f0 denovo3588_f0 denovo3614_f0 denovo3666_f0 denovo3692_f0 denovo3718_f0 denovo3770_f0 denovo3848_f0 denovo3952_f0 denovo3978_f0 denovo4030_f0 denovo4056_f0 denovo4186_f0 denovo4290_f0 denovo4316_f0 denovo4342_f0 denovo4394_f0 denovo4446_f0 denovo4550_f0 denovo4628_f0 denovo4732_f0 denovo4758_f0 denovo4784_f0 denovo4836_f0 denovo4888_f0 denovo4914_f0 denovo4940_f0 denovo4966_f0 denovo4992_f0 denovo5200_f0 denovo5226_f0 denovo5252_f0 denovo5382_f0 denovo5434_f0 denovo5512_f0 denovo5590_f0 denovo5616_f0 denovo5642_f0 denovo5928_f0 denovo6006_f0 denovo6058_f0 denovo6110_f0 denovo6214_f0 denovo6240_f0 denovo6266_f0 denovo6578_f0 denovo6604_f0 denovo6682_f0 denovo6708_f0 denovo6760_f0 denovo6812_f0 denovo6864_f0 denovo6994_f0 denovo7072_f0 denovo7124_f0 denovo7150_f0 denovo7254_f0 denovo7332_f0 denovo7384_f0 denovo7410_f0 denovo7514_f0 denovo7540_f0 denovo7566_f0 denovo7618_f0 denovo7670_f0 denovo7696_f0 denovo7748_f0 denovo7800_f0 denovo7982_f0 denovo8034_f0 denovo8060_f0 denovo8216_f0 denovo8242_f0 denovo8268_f0 denovo8294_f0 denovo8398_f0 denovo8424_f0 denovo8450_f0 denovo8580_f0 denovo8632_f0 denovo8658_f0 denovo8684_f0 denovo8762_f0 denovo8814_f0 denovo8840_f0 denovo8892_f0 denovo8918_f0 denovo8944_f0 denovo8970_f0 denovo8996_f0 denovo9126_f0 denovo9152_f0 denovo9178_f0 denovo9308_f0 denovo9334_f0 denovo9360_f0 denovo9386_f0 denovo9438_f0 denovo9490_f0 denovo9542_f0 denovo9594_f0 denovo9672_f0 denovo9698_f0 denovo9724_f0 denovo9802_f0 denovo9828_f0 denovo9854_f0 denovo9880_f0 denovo9932_f0 denovo9958_f0 denovo9984_f0 denovo10062_f0 denovo10166_f0 denovo10192_f0 denovo10218_f0 denovo10270_f0 denovo10296_f0 denovo10348_f0 denovo10374_f0 denovo10400_f0 denovo10426_f0 denovo10478_f0 denovo10504_f0 denovo10530_f0 denovo10608_f0 denovo10660_f0 denovo10686_f0 denovo10764_f0 denovo10842_f0 denovo10868_f0 denovo10920_f0 denovo10972_f0 denovo11024_f0 denovo11076_f0 denovo11102_f0 denovo11154_f0 denovo11180_f0 denovo11232_f0 denovo11258_f0 denovo11310_f0 denovo11336_f0 denovo11440_f0 denovo11544_f0 denovo11908_f0 denovo11960_f0 denovo12064_f0 Pcit2 denovo45_f0 denovo97_f0 denovo123_f0 denovo149_f0 denovo227_f0 denovo253_f0 denovo279_f0 denovo305_f0 denovo357_f0 denovo435_f0 denovo539_f0 denovo591_f0 denovo617_f0 denovo747_f0 denovo799_f0 denovo955_f0 denovo981_f0 denovo1059_f0 denovo1085_f0 denovo1163_f0 denovo1319_f0 denovo1501_f0 denovo1527_f0 denovo1657_f0 denovo1761_f0 denovo1787_f0 denovo1813_f0 denovo1969_f0 denovo2151_f0 denovo2203_f0 denovo2255_f0 denovo2281_f0 denovo2359_f0 denovo2463_f0 denovo2489_f0 denovo2515_f0 denovo2541_f0 denovo2593_f0 denovo2619_f0 denovo2671_f0 denovo2775_f0 denovo2801_f0 denovo2853_f0 denovo2879_f0 denovo2931_f0 denovo3009_f0 denovo3061_f0 denovo3165_f0 denovo3243_f0 denovo3269_f0 denovo3295_f0 denovo3321_f0 denovo3347_f0 denovo3451_f0 denovo3503_f0 denovo3607_f0 denovo3633_f0 denovo3685_f0 denovo3711_f0 denovo3737_f0 denovo3789_f0 denovo3867_f0 denovo3971_f0 denovo3997_f0 denovo4049_f0 denovo4075_f0 denovo4205_f0 denovo4309_f0 denovo4335_f0 denovo4361_f0 denovo4413_f0 denovo4465_f0 denovo4569_f0 denovo4647_f0 denovo4751_f0 denovo4777_f0 denovo4803_f0 denovo4855_f0 denovo4907_f0 denovo4933_f0 denovo4959_f0 denovo4985_f0 denovo5011_f0 denovo5219_f0 denovo5245_f0 denovo5271_f0 denovo5401_f0 denovo5453_f0 denovo5531_f0 denovo5609_f0 denovo5635_f0 denovo5661_f0 denovo5947_f0 denovo6025_f0 denovo6077_f0 denovo6129_f0 denovo6233_f0 denovo6259_f0 denovo6285_f0 denovo6597_f0 denovo6623_f0 denovo6701_f0 denovo6727_f0 denovo6779_f0 denovo6831_f0 denovo6883_f0 denovo7013_f0 denovo7091_f0 denovo7143_f0 denovo7169_f0 denovo7273_f0 denovo7351_f0 denovo7403_f0 denovo7429_f0 denovo7533_f0 denovo7559_f0 denovo7585_f0 denovo7637_f0 denovo7689_f0 denovo7715_f0 denovo7767_f0 denovo7819_f0 denovo8001_f0 denovo8053_f0 denovo8079_f0 denovo8235_f0 denovo8261_f0 denovo8287_f0 denovo8313_f0 denovo8417_f0 denovo8443_f0 denovo8469_f0 denovo8599_f0 denovo8651_f0 denovo8677_f0 denovo8703_f0 denovo8781_f0 denovo8833_f0 denovo8859_f0 denovo8911_f0 denovo8937_f0 denovo8963_f0 denovo8989_f0 denovo9015_f0 denovo9145_f0 denovo9171_f0 denovo9197_f0 denovo9327_f0 denovo9353_f0 denovo9379_f0 denovo9405_f0 denovo9457_f0 denovo9509_f0 denovo9561_f0 denovo9613_f0 denovo9691_f0 denovo9717_f0 denovo9743_f0 denovo9821_f0 denovo9847_f0 denovo9873_f0 denovo9899_f0 denovo9951_f0 denovo9977_f0 denovo10003_f0 denovo10081_f0 denovo10185_f0 denovo10211_f0 denovo10237_f0 denovo10289_f0 denovo10315_f0 denovo10367_f0 denovo10393_f0 denovo10419_f0 denovo10445_f0 denovo10497_f0 denovo10523_f0 denovo10549_f0 denovo10627_f0 denovo10679_f0 denovo10705_f0 denovo10783_f0 denovo10861_f0 denovo10887_f0 denovo10939_f0 denovo10991_f0 denovo11043_f0 denovo11095_f0 denovo11121_f0 denovo11173_f0 denovo11199_f0 denovo11251_f0 denovo11277_f0 denovo11329_f0 denovo11355_f0 denovo11459_f0 denovo11563_f0 denovo11927_f0 denovo11979_f0 denovo12083_f0 Concatenation entropy_0.48_0.00_loci_50_to_249 will have the following data OTU EOG69CQC1_1 EOG6SN1SH_1 EOG6PRSVJ_1 EOG680J15_1 EOG60ZR1Z_1 EOG60P4BD_1 EOG64QT4T_1 EOG6NCMGZ_1 EOG6K3M19_1 EOG60P4BJ_1 EOG6DBTK0_1 EOG6GTKHJ_1 EOG68KRFS_1 EOG6GHZSR_1 EOG666VQ4_1 EOG698V44_1 EOG6894QQ_1 EOG6868GW_1 EOG69PB31_1 EOG6JDHBD_1 EOG63212K_1 EOG68D102_1 EOG60ZR1T_1 EOG6CJVMH_1 EOG698V46_1 EOG68KRG8_1 EOG6N8R81_1 EOG63BMSV_1 EOG69KFV1_1 EOG6CC44S_1 EOG6FXRCK_1 EOG6R2400_1 EOG68KRG4_1 EOG61C70T_1 EOG6BK575_1 EOG63212W_1 EOG6F7NPJ_1 EOG695ZW4_1 EOG61NTQM_1 EOG6NZTZ3_1 EOG6J3WM7_1 EOG680J16_1 EOG68SGXM_1 EOG6RNBCT_1 EOG6RFKXS_1 EOG67SSJJ_1 EOG69GKKW_1 EOG6QFWHZ_1 EOG6RFKXB_1 EOG647FXX_1 EOG6B8JHP_1 EOG6S1TBX_1 EOG6DFPRT_1 EOG65HS25_1 EOG6FFD5C_1 EOG6R506D_1 EOG6F4SFZ_1 EOG6Q8524_1 EOG6QVCGP_1 EOG669QZR_1 EOG6JT09B_1 EOG65TCRS_1 EOG6QRH88_1 EOG6M65N6_1 EOG6QRH81_1 EOG6RJG4W_1 EOG6KKZ6X_1 EOG60VVTG_1 EOG6QC198_1 EOG6D26TG_1 EOG679FBS_1 EOG61RPZF_1 EOG6PC9WG_1 EOG60GCVD_1 EOG6R506Q_1 EOG605S4X_1 EOG65TCRN_1 EOG608ND4_1 EOG6640GX_1 EOG6SQX12_1 EOG69GKMS_1 EOG6D26TV_1 EOG605S4Z_1 EOG6N04JN_1 EOG64TPCQ_1 EOG6NP76T_1 EOG67H5V2_1 EOG66DM62_1 EOG6QFWJH_1 EOG6N04K4_1 EOG69KFTV_1 EOG6CJVMQ_1 EOG62V8KS_1 EOG6DZ204_1 EOG6C5CPH_1 EOG6FFD51_1 EOG6QNN0J_1 EOG6KSPP5_1 EOG6N5W22_1 EOG6PK2CG_1 EOG6NP779_1 EOG6933N9_1 EOG66Q6XP_1 EOG6JQ427_1 EOG6C5CNP_1 EOG6R5066_1 EOG6FTW4C_1 EOG65B1K2_1 EOG66WZD1_1 EOG6FR0WR_1 EOG6P2Q64_1 EOG666VQC_1 EOG63R3R5_1 EOG6PC9WF_1 EOG6Q58T0_1 EOG641QGH_1 EOG6933N7_1 EOG69S6BG_1 EOG6NS3FV_1 EOG65MN9B_1 EOG641QFW_1 EOG6N04J6_1 EOG6GMV1P_1 EOG6S4PKX_1 EOG6BZN62_1 EOG6SXNGX_1 EOG6CG0CT_1 EOG6HHP6B_1 EOG605S4Q_1 EOG6R7VF9_1 EOG6CZBM5_1 EOG6JT092_1 EOG64F6DK_1 EOG6FJ8D6_1 EOG6QZ7QX_1 EOG6F1X6M_1 EOG67PX9B_1 EOG6SBF2V_1 EOG6KSPQ0_1 EOG6GMV1H_1 EOG63R3RC_1 EOG68SGX8_1 EOG60K83N_1 EOG6KD6Q9_1 EOG68GW6Q_1 EOG6Q852G_1 EOG676K44_1 EOG6FN4NZ_1 EOG6S1TC2_1 EOG6HT8WD_1 EOG63FH1F_1 EOG6CRM3H_1 EOG6PRSVP_1 EOG6R5069_1 EOG6CC453_1 EOG6001PC_1 EOG676K40_1 EOG6N30SN_1 EOG6255XM_1 EOG64BB5X_1 EOG62FSN7_1 EOG6H72G0_1 EOG6PZJB1_1 EOG65QHHP_1 EOG615GHV_1 EOG62BXCZ_1 EOG6CG0D0_1 EOG69KFVF_1 EOG615GHP_1 EOG683D8Q_1 EOG64J2NS_1 EOG66HGF5_1 EOG6DFPSF_1 EOG66MBPR_1 EOG6DFPSD_1 EOG64BB5N_1 EOG6DBTJX_1 EOG6DBTHZ_1 EOG6KH2ZD_1 EOG6STS87_1 EOG67D9KV_1 EOG6SXNHG_1 EOG6GF3JF_1 EOG61RPZ9_1 EOG637RJP_1 EOG6J3WMR_1 EOG6GB79H_1 EOG6JDHBG_1 EOG6DV5QM_1 EOG6GTKHQ_1 EOG6FR0W5_1 EOG6K0QRT_1 EOG65DWSM_1 EOG6CC452_1 EOG6G4GTX_1 EOG61G37F_1 EOG6FFD5V_1 EOG6G4GTT_1 EOG6GXFR5_1 EOG6KPTG0_1 Dplexcds denovo2_f0 denovo80_f0 denovo158_f0 denovo210_f0 denovo262_f0 denovo366_f0 denovo418_f0 denovo444_f0 denovo522_f0 denovo574_f0 denovo600_f0 denovo782_f0 denovo1042_f0 denovo1068_f0 denovo1146_f0 denovo1224_f0 denovo1354_f0 denovo1380_f0 denovo1406_f0 denovo1484_f0 denovo1510_f0 denovo1640_f0 denovo1666_f0 denovo1744_f0 denovo1796_f0 denovo1926_f0 denovo1952_f0 denovo1978_f0 denovo2004_f0 denovo2108_f0 denovo2134_f0 denovo2186_f0 denovo2238_f0 denovo2264_f0 denovo2290_f0 denovo2446_f0 denovo2472_f0 denovo2498_f0 denovo2524_f0 denovo2576_f0 denovo2602_f0 denovo2628_f0 denovo2654_f0 denovo2758_f0 denovo2836_f0 denovo2914_f0 denovo2992_f0 denovo3148_f0 denovo3252_f0 denovo3304_f0 denovo3330_f0 denovo3434_f0 denovo3486_f0 denovo3590_f0 denovo3616_f0 denovo3668_f0 denovo3720_f0 denovo3746_f0 denovo3772_f0 denovo3798_f0 denovo3824_f0 denovo3850_f0 denovo3954_f0 denovo3980_f0 denovo4058_f0 denovo4188_f0 denovo4318_f0 denovo4344_f0 denovo4370_f0 denovo4396_f0 denovo4552_f0 denovo4630_f0 denovo4734_f0 denovo4760_f0 denovo4786_f0 denovo4838_f0 denovo4890_f0 denovo4916_f0 denovo4942_f0 denovo4968_f0 denovo4994_f0 denovo5202_f0 denovo5228_f0 denovo5254_f0 denovo5436_f0 denovo5592_f0 denovo5644_f0 denovo5956_f0 denovo6008_f0 denovo6060_f0 denovo6086_f0 denovo6112_f0 denovo6190_f0 denovo6216_f0 denovo6242_f0 denovo6268_f0 denovo6294_f0 denovo6372_f0 denovo6502_f0 denovo6554_f0 denovo6580_f0 denovo6606_f0 denovo6658_f0 denovo6684_f0 denovo6710_f0 denovo6736_f0 denovo6762_f0 denovo6970_f0 denovo6996_f0 denovo7074_f0 denovo7126_f0 denovo7152_f0 denovo7256_f0 denovo7282_f0 denovo7308_f0 denovo7334_f0 denovo7360_f0 denovo7386_f0 denovo7490_f0 denovo7516_f0 denovo7542_f0 denovo7620_f0 denovo7672_f0 denovo7698_f0 denovo7828_f0 denovo7906_f0 denovo8036_f0 denovo8062_f0 denovo8218_f0 denovo8244_f0 denovo8270_f0 denovo8296_f0 denovo8374_f0 denovo8400_f0 denovo8426_f0 denovo8452_f0 denovo8556_f0 denovo8582_f0 denovo8634_f0 denovo8660_f0 denovo8686_f0 denovo8764_f0 denovo8842_f0 denovo8894_f0 denovo8920_f0 denovo8946_f0 denovo8972_f0 denovo8998_f0 denovo9128_f0 denovo9154_f0 denovo9180_f0 denovo9284_f0 denovo9310_f0 denovo9336_f0 denovo9362_f0 denovo9388_f0 denovo9440_f0 denovo9492_f0 denovo9700_f0 denovo9726_f0 denovo9778_f0 denovo9804_f0 denovo9830_f0 denovo9882_f0 denovo9960_f0 denovo10194_f0 denovo10220_f0 denovo10272_f0 denovo10298_f0 denovo10350_f0 denovo10402_f0 denovo10428_f0 denovo10454_f0 denovo10506_f0 denovo10532_f0 denovo10610_f0 denovo10662_f0 denovo10714_f0 denovo10740_f0 denovo10766_f0 denovo10818_f0 denovo10844_f0 denovo10922_f0 denovo11000_f0 denovo11026_f0 denovo11078_f0 denovo11156_f0 denovo11182_f0 denovo11286_f0 denovo11312_f0 denovo11338_f0 denovo11390_f0 denovo11416_f0 denovo11442_f0 denovo11468_f0 denovo11546_f0 denovo11702_f0 denovo11728_f0 denovo11910_f0 denovo12066_f0 FG120077 denovo10_f0 denovo88_f0 denovo166_f0 denovo218_f0 denovo270_f0 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denovo8261_f0 denovo8287_f0 denovo8313_f0 denovo8391_f0 denovo8417_f0 denovo8443_f0 denovo8469_f0 denovo8573_f0 denovo8599_f0 denovo8651_f0 denovo8677_f0 denovo8703_f0 denovo8781_f0 denovo8859_f0 denovo8911_f0 denovo8937_f0 denovo8963_f0 denovo8989_f0 denovo9015_f0 denovo9145_f0 denovo9171_f0 denovo9197_f0 denovo9301_f0 denovo9327_f0 denovo9353_f0 denovo9379_f0 denovo9405_f0 denovo9457_f0 denovo9509_f0 denovo9717_f0 denovo9743_f0 denovo9795_f0 denovo9821_f0 denovo9847_f0 denovo9899_f0 denovo9977_f0 denovo10211_f0 denovo10237_f0 denovo10289_f0 denovo10315_f0 denovo10367_f0 denovo10419_f0 denovo10445_f0 denovo10471_f0 denovo10523_f0 denovo10549_f0 denovo10627_f0 denovo10679_f0 denovo10731_f0 denovo10757_f0 denovo10783_f0 denovo10835_f0 denovo10861_f0 denovo10939_f0 denovo11017_f0 denovo11043_f0 denovo11095_f0 denovo11173_f0 denovo11199_f0 denovo11303_f0 denovo11329_f0 denovo11355_f0 denovo11407_f0 denovo11433_f0 denovo11459_f0 denovo11485_f0 denovo11563_f0 denovo11719_f0 denovo11745_f0 denovo11927_f0 denovo12083_f0 Concatenation entropy_0.30_0.00_loci_100_to_299 will have the following data OTU EOG69CQC1_1 EOG6SN1SH_1 EOG6PRSVJ_1 EOG6PRSVH_1 EOG60ZR1Z_1 EOG6FXRCN_1 EOG60P4BD_1 EOG6NCMGZ_1 EOG6K3M19_1 EOG63TZZV_1 EOG6G7C30_1 EOG68KRFS_1 EOG666VQ4_1 EOG698V44_1 EOG6F7NPM_1 EOG6894QQ_1 EOG6868GW_1 EOG69PB31_1 EOG6JDHBD_1 EOG68D102_1 EOG60ZR1T_1 EOG63JC89_1 EOG698V46_1 EOG6J6RV9_1 EOG68KRG8_1 EOG6N8R81_1 EOG63BMSV_1 EOG69KFV1_1 EOG6C2HF4_1 EOG6CC44S_1 EOG6FXRCK_1 EOG68KRG4_1 EOG61C70T_1 EOG6BK575_1 EOG6R506X_1 EOG6JT09G_1 EOG6F7NPJ_1 EOG61NTQM_1 EOG6SJ5J3_1 EOG6NZTZ3_1 EOG6J3WM7_1 EOG680J16_1 EOG68SGXM_1 EOG6RNBCT_1 EOG6RFKXS_1 EOG6B8JHB_1 EOG6QFWHZ_1 EOG6RFKXB_1 EOG647FXX_1 EOG6B8JHP_1 EOG6S1TBX_1 EOG6DFPRT_1 EOG65HS25_1 EOG6FFD5C_1 EOG6PNXM9_1 EOG6F4SFZ_1 EOG6Q8524_1 EOG669QZR_1 EOG6JT09B_1 EOG6M65N6_1 EOG6QRH81_1 EOG65HS1N_1 EOG6FR0VW_1 EOG6KKZ6X_1 EOG60VVTG_1 EOG6QC198_1 EOG6D26TG_1 EOG6FFD52_1 EOG634W9K_1 EOG6DNF7N_1 EOG61RPZF_1 EOG60GCVD_1 EOG605S4X_1 EOG65TCRN_1 EOG608ND4_1 EOG6640GX_1 EOG6SQX12_1 EOG69GKMS_1 EOG6B8JHC_1 EOG6Q2DJZ_1 EOG6D26TV_1 EOG6NS3G8_1 EOG64TPCQ_1 EOG6229Q2_1 EOG63TZZW_1 EOG6BG90S_1 EOG66DM62_1 EOG6QFWJH_1 EOG69CQBW_1 EOG6N04K4_1 EOG69KFTV_1 EOG62V8KS_1 EOG6C5CPH_1 EOG6FFD51_1 EOG6QNN0J_1 EOG6KSPP5_1 EOG6N5W22_1 EOG6PK2CG_1 EOG6NP779_1 EOG6933N9_1 EOG66Q6XP_1 EOG6JQ427_1 EOG6C5CNP_1 EOG6R5066_1 EOG6FTW4C_1 EOG641QFN_1 EOG65B1K2_1 EOG66WZD1_1 EOG65TCRK_1 EOG6FR0WR_1 EOG6P2Q64_1 EOG666VQC_1 EOG6PC9WF_1 EOG6Q58T0_1 EOG641QGH_1 EOG6933N7_1 EOG69S6BG_1 EOG6PK2CM_1 EOG6NS3FV_1 EOG65MN9B_1 EOG641QFW_1 EOG6N04J6_1 EOG6GMV1P_1 EOG6S4PKX_1 EOG6K6G7S_1 EOG6BZN62_1 EOG6SXNGX_1 EOG6QC18P_1 EOG6CG0CT_1 EOG605S4Q_1 EOG6R7VF9_1 EOG6CZBM5_1 EOG63R3RK_1 EOG64F6DK_1 EOG6FJ8D6_1 EOG6001NN_1 EOG695ZWC_1 EOG67PX9B_1 EOG6P8FNH_1 EOG6KSPQ0_1 EOG63R3RC_1 EOG6907D7_1 EOG6JWVHT_1 EOG68SGX8_1 EOG6KD6Q9_1 EOG68GW6Q_1 EOG6Q852G_1 EOG676K44_1 EOG64MXWZ_1 EOG6S1TC2_1 EOG6Q58SW_1 EOG6CRM3H_1 EOG6PRSVP_1 EOG6R5069_1 EOG676K40_1 EOG64MXWK_1 EOG6N30SN_1 EOG6DR9GZ_1 EOG6255XM_1 EOG62FSN7_1 EOG6H72G0_1 EOG6PZJB1_1 EOG65QHHP_1 EOG615GHV_1 EOG66WZCQ_1 EOG698V4H_1 EOG62BXCZ_1 EOG6CG0D0_1 EOG69KFVF_1 EOG615GHP_1 EOG66HGF5_1 EOG6DFPSF_1 EOG66MBPR_1 EOG6DFPSD_1 EOG67D9KC_1 EOG6HHP5S_1 EOG6DBTJX_1 EOG6DBTHZ_1 EOG6KH2ZD_1 EOG6STS87_1 EOG67D9KV_1 EOG61RPZ9_1 EOG637RJP_1 EOG66MBP7_1 EOG6JDHBG_1 EOG6DV5QM_1 EOG6FR0W5_1 EOG6K0QRT_1 EOG65DWSM_1 EOG6CC452_1 EOG6G4GTX_1 EOG64BB5H_1 EOG64J2NC_1 EOG6H72G3_1 EOG6SBF2B_1 EOG6FFD5V_1 EOG6G4GTT_1 EOG6GXFR5_1 EOG61C70W_1 EOG6KPTG0_1 Dplexcds denovo2_f0 denovo80_f0 denovo158_f0 denovo184_f0 denovo262_f0 denovo314_f0 denovo366_f0 denovo444_f0 denovo522_f0 denovo678_f0 denovo834_f0 denovo1042_f0 denovo1146_f0 denovo1224_f0 denovo1250_f0 denovo1354_f0 denovo1380_f0 denovo1406_f0 denovo1484_f0 denovo1640_f0 denovo1666_f0 denovo1718_f0 denovo1796_f0 denovo1848_f0 denovo1926_f0 denovo1952_f0 denovo1978_f0 denovo2004_f0 denovo2082_f0 denovo2108_f0 denovo2134_f0 denovo2238_f0 denovo2264_f0 denovo2290_f0 denovo2316_f0 denovo2368_f0 denovo2472_f0 denovo2524_f0 denovo2550_f0 denovo2576_f0 denovo2602_f0 denovo2628_f0 denovo2654_f0 denovo2758_f0 denovo2836_f0 denovo2888_f0 denovo3148_f0 denovo3252_f0 denovo3304_f0 denovo3330_f0 denovo3434_f0 denovo3486_f0 denovo3590_f0 denovo3616_f0 denovo3642_f0 denovo3720_f0 denovo3746_f0 denovo3798_f0 denovo3824_f0 denovo3980_f0 denovo4058_f0 denovo4136_f0 denovo4240_f0 denovo4318_f0 denovo4344_f0 denovo4370_f0 denovo4396_f0 denovo4422_f0 denovo4500_f0 denovo4526_f0 denovo4630_f0 denovo4760_f0 denovo4838_f0 denovo4890_f0 denovo4916_f0 denovo4942_f0 denovo4968_f0 denovo4994_f0 denovo5098_f0 denovo5150_f0 denovo5202_f0 denovo5410_f0 denovo5436_f0 denovo5540_f0 denovo5566_f0 denovo5904_f0 denovo5956_f0 denovo6008_f0 denovo6034_f0 denovo6060_f0 denovo6086_f0 denovo6190_f0 denovo6242_f0 denovo6268_f0 denovo6294_f0 denovo6372_f0 denovo6502_f0 denovo6554_f0 denovo6580_f0 denovo6606_f0 denovo6658_f0 denovo6684_f0 denovo6710_f0 denovo6736_f0 denovo6762_f0 denovo6892_f0 denovo6970_f0 denovo6996_f0 denovo7022_f0 denovo7074_f0 denovo7126_f0 denovo7152_f0 denovo7282_f0 denovo7308_f0 denovo7334_f0 denovo7360_f0 denovo7386_f0 denovo7464_f0 denovo7490_f0 denovo7516_f0 denovo7542_f0 denovo7620_f0 denovo7672_f0 denovo7698_f0 denovo7776_f0 denovo7828_f0 denovo7906_f0 denovo8010_f0 denovo8036_f0 denovo8218_f0 denovo8244_f0 denovo8270_f0 denovo8348_f0 denovo8374_f0 denovo8400_f0 denovo8478_f0 denovo8530_f0 denovo8556_f0 denovo8608_f0 denovo8634_f0 denovo8686_f0 denovo8712_f0 denovo8738_f0 denovo8764_f0 denovo8894_f0 denovo8920_f0 denovo8946_f0 denovo8972_f0 denovo9102_f0 denovo9128_f0 denovo9232_f0 denovo9284_f0 denovo9310_f0 denovo9336_f0 denovo9440_f0 denovo9466_f0 denovo9492_f0 denovo9648_f0 denovo9700_f0 denovo9778_f0 denovo9804_f0 denovo9830_f0 denovo9882_f0 denovo9960_f0 denovo10012_f0 denovo10038_f0 denovo10194_f0 denovo10220_f0 denovo10272_f0 denovo10298_f0 denovo10428_f0 denovo10454_f0 denovo10506_f0 denovo10532_f0 denovo10558_f0 denovo10584_f0 denovo10662_f0 denovo10714_f0 denovo10740_f0 denovo10766_f0 denovo10818_f0 denovo11000_f0 denovo11026_f0 denovo11052_f0 denovo11182_f0 denovo11286_f0 denovo11338_f0 denovo11390_f0 denovo11416_f0 denovo11442_f0 denovo11468_f0 denovo11494_f0 denovo11520_f0 denovo11572_f0 denovo11598_f0 denovo11702_f0 denovo11728_f0 denovo11910_f0 denovo11936_f0 denovo12066_f0 FG120077 denovo10_f0 denovo88_f0 denovo166_f0 denovo192_f0 denovo270_f0 denovo322_f0 denovo374_f0 denovo452_f0 denovo530_f0 denovo686_f0 denovo842_f0 denovo1050_f0 denovo1154_f0 denovo1232_f0 denovo1258_f0 denovo1362_f0 denovo1388_f0 denovo1414_f0 denovo1492_f0 denovo1648_f0 denovo1674_f0 denovo1726_f0 denovo1804_f0 denovo1856_f0 denovo1934_f0 denovo1960_f0 denovo1986_f0 denovo2012_f0 denovo2090_f0 denovo2116_f0 denovo2142_f0 denovo2246_f0 denovo2272_f0 denovo2298_f0 denovo2324_f0 denovo2376_f0 denovo2480_f0 denovo2532_f0 denovo2558_f0 denovo2584_f0 denovo2610_f0 denovo2636_f0 denovo2662_f0 denovo2766_f0 denovo2844_f0 denovo2896_f0 denovo3156_f0 denovo3260_f0 denovo3312_f0 denovo3338_f0 denovo3442_f0 denovo3494_f0 denovo3598_f0 denovo3624_f0 denovo3650_f0 denovo3728_f0 denovo3754_f0 denovo3806_f0 denovo3832_f0 denovo3988_f0 denovo4066_f0 denovo4144_f0 denovo4248_f0 denovo4326_f0 denovo4352_f0 denovo4378_f0 denovo4404_f0 denovo4430_f0 denovo4508_f0 denovo4534_f0 denovo4638_f0 denovo4768_f0 denovo4846_f0 denovo4898_f0 denovo4924_f0 denovo4950_f0 denovo4976_f0 denovo5002_f0 denovo5106_f0 denovo5158_f0 denovo5210_f0 denovo5418_f0 denovo5444_f0 denovo5548_f0 denovo5574_f0 denovo5912_f0 denovo5964_f0 denovo6016_f0 denovo6042_f0 denovo6068_f0 denovo6094_f0 denovo6198_f0 denovo6250_f0 denovo6276_f0 denovo6302_f0 denovo6380_f0 denovo6510_f0 denovo6562_f0 denovo6588_f0 denovo6614_f0 denovo6666_f0 denovo6692_f0 denovo6718_f0 denovo6744_f0 denovo6770_f0 denovo6900_f0 denovo6978_f0 denovo7004_f0 denovo7030_f0 denovo7082_f0 denovo7134_f0 denovo7160_f0 denovo7290_f0 denovo7316_f0 denovo7342_f0 denovo7368_f0 denovo7394_f0 denovo7472_f0 denovo7498_f0 denovo7524_f0 denovo7550_f0 denovo7628_f0 denovo7680_f0 denovo7706_f0 denovo7784_f0 denovo7836_f0 denovo7914_f0 denovo8018_f0 denovo8044_f0 denovo8226_f0 denovo8252_f0 denovo8278_f0 denovo8356_f0 denovo8382_f0 denovo8408_f0 denovo8486_f0 denovo8538_f0 denovo8564_f0 denovo8616_f0 denovo8642_f0 denovo8694_f0 denovo8720_f0 denovo8746_f0 denovo8772_f0 denovo8902_f0 denovo8928_f0 denovo8954_f0 denovo8980_f0 denovo9110_f0 denovo9136_f0 denovo9240_f0 denovo9292_f0 denovo9318_f0 denovo9344_f0 denovo9448_f0 denovo9474_f0 denovo9500_f0 denovo9656_f0 denovo9708_f0 denovo9786_f0 denovo9812_f0 denovo9838_f0 denovo9890_f0 denovo9968_f0 denovo10020_f0 denovo10046_f0 denovo10202_f0 denovo10228_f0 denovo10280_f0 denovo10306_f0 denovo10436_f0 denovo10462_f0 denovo10514_f0 denovo10540_f0 denovo10566_f0 denovo10592_f0 denovo10670_f0 denovo10722_f0 denovo10748_f0 denovo10774_f0 denovo10826_f0 denovo11008_f0 denovo11034_f0 denovo11060_f0 denovo11190_f0 denovo11294_f0 denovo11346_f0 denovo11398_f0 denovo11424_f0 denovo11450_f0 denovo11476_f0 denovo11502_f0 denovo11528_f0 denovo11580_f0 denovo11606_f0 denovo11710_f0 denovo11736_f0 denovo11918_f0 denovo11944_f0 denovo12074_f0 SRR803483 denovo20_f0 denovo98_f0 denovo176_f0 denovo202_f0 denovo280_f0 denovo332_f0 denovo384_f0 denovo462_f0 denovo540_f0 denovo696_f0 denovo852_f0 denovo1060_f0 denovo1164_f0 denovo1242_f0 denovo1268_f0 denovo1372_f0 denovo1398_f0 denovo1424_f0 denovo1502_f0 denovo1658_f0 denovo1684_f0 denovo1736_f0 denovo1814_f0 denovo1866_f0 denovo1944_f0 denovo1970_f0 denovo1996_f0 denovo2022_f0 denovo2100_f0 denovo2126_f0 denovo2152_f0 denovo2256_f0 denovo2282_f0 denovo2308_f0 denovo2334_f0 denovo2386_f0 denovo2490_f0 denovo2542_f0 denovo2568_f0 denovo2594_f0 denovo2620_f0 denovo2646_f0 denovo2672_f0 denovo2776_f0 denovo2854_f0 denovo2906_f0 denovo3166_f0 denovo3270_f0 denovo3322_f0 denovo3348_f0 denovo3452_f0 denovo3504_f0 denovo3608_f0 denovo3634_f0 denovo3660_f0 denovo3738_f0 denovo3764_f0 denovo3816_f0 denovo3842_f0 denovo3998_f0 denovo4076_f0 denovo4154_f0 denovo4258_f0 denovo4336_f0 denovo4362_f0 denovo4388_f0 denovo4414_f0 denovo4440_f0 denovo4518_f0 denovo4544_f0 denovo4648_f0 denovo4778_f0 denovo4856_f0 denovo4908_f0 denovo4934_f0 denovo4960_f0 denovo4986_f0 denovo5012_f0 denovo5116_f0 denovo5168_f0 denovo5220_f0 denovo5428_f0 denovo5454_f0 denovo5558_f0 denovo5584_f0 denovo5922_f0 denovo5974_f0 denovo6026_f0 denovo6052_f0 denovo6078_f0 denovo6104_f0 denovo6208_f0 denovo6260_f0 denovo6286_f0 denovo6312_f0 denovo6390_f0 denovo6520_f0 denovo6572_f0 denovo6598_f0 denovo6624_f0 denovo6676_f0 denovo6702_f0 denovo6728_f0 denovo6754_f0 denovo6780_f0 denovo6910_f0 denovo6988_f0 denovo7014_f0 denovo7040_f0 denovo7092_f0 denovo7144_f0 denovo7170_f0 denovo7300_f0 denovo7326_f0 denovo7352_f0 denovo7378_f0 denovo7404_f0 denovo7482_f0 denovo7508_f0 denovo7534_f0 denovo7560_f0 denovo7638_f0 denovo7690_f0 denovo7716_f0 denovo7794_f0 denovo7846_f0 denovo7924_f0 denovo8028_f0 denovo8054_f0 denovo8236_f0 denovo8262_f0 denovo8288_f0 denovo8366_f0 denovo8392_f0 denovo8418_f0 denovo8496_f0 denovo8548_f0 denovo8574_f0 denovo8626_f0 denovo8652_f0 denovo8704_f0 denovo8730_f0 denovo8756_f0 denovo8782_f0 denovo8912_f0 denovo8938_f0 denovo8964_f0 denovo8990_f0 denovo9120_f0 denovo9146_f0 denovo9250_f0 denovo9302_f0 denovo9328_f0 denovo9354_f0 denovo9458_f0 denovo9484_f0 denovo9510_f0 denovo9666_f0 denovo9718_f0 denovo9796_f0 denovo9822_f0 denovo9848_f0 denovo9900_f0 denovo9978_f0 denovo10030_f0 denovo10056_f0 denovo10212_f0 denovo10238_f0 denovo10290_f0 denovo10316_f0 denovo10446_f0 denovo10472_f0 denovo10524_f0 denovo10550_f0 denovo10576_f0 denovo10602_f0 denovo10680_f0 denovo10732_f0 denovo10758_f0 denovo10784_f0 denovo10836_f0 denovo11018_f0 denovo11044_f0 denovo11070_f0 denovo11200_f0 denovo11304_f0 denovo11356_f0 denovo11408_f0 denovo11434_f0 denovo11460_f0 denovo11486_f0 denovo11512_f0 denovo11538_f0 denovo11590_f0 denovo11616_f0 denovo11720_f0 denovo11746_f0 denovo11928_f0 denovo11954_f0 denovo12084_f0 FG120035 denovo5_f0 denovo83_f0 denovo161_f0 denovo187_f0 denovo265_f0 denovo317_f0 denovo369_f0 denovo447_f0 denovo525_f0 denovo681_f0 denovo837_f0 denovo1045_f0 denovo1149_f0 denovo1227_f0 denovo1253_f0 denovo1357_f0 denovo1383_f0 denovo1409_f0 denovo1487_f0 denovo1643_f0 denovo1669_f0 denovo1721_f0 denovo1799_f0 denovo1851_f0 denovo1929_f0 denovo1955_f0 denovo1981_f0 denovo2007_f0 denovo2085_f0 denovo2111_f0 denovo2137_f0 denovo2241_f0 denovo2267_f0 denovo2293_f0 denovo2319_f0 denovo2371_f0 denovo2475_f0 denovo2527_f0 denovo2553_f0 denovo2579_f0 denovo2605_f0 denovo2631_f0 denovo2657_f0 denovo2761_f0 denovo2839_f0 denovo2891_f0 denovo3151_f0 denovo3255_f0 denovo3307_f0 denovo3333_f0 denovo3437_f0 denovo3489_f0 denovo3593_f0 denovo3619_f0 denovo3645_f0 denovo3723_f0 denovo3749_f0 denovo3801_f0 denovo3827_f0 denovo3983_f0 denovo4061_f0 denovo4139_f0 denovo4243_f0 denovo4321_f0 denovo4347_f0 denovo4373_f0 denovo4399_f0 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denovo832_f0 denovo1040_f0 denovo1144_f0 denovo1222_f0 denovo1248_f0 denovo1352_f0 denovo1378_f0 denovo1404_f0 denovo1482_f0 denovo1638_f0 denovo1664_f0 denovo1716_f0 denovo1794_f0 denovo1846_f0 denovo1924_f0 denovo1950_f0 denovo1976_f0 denovo2002_f0 denovo2080_f0 denovo2106_f0 denovo2132_f0 denovo2236_f0 denovo2262_f0 denovo2288_f0 denovo2314_f0 denovo2366_f0 denovo2470_f0 denovo2522_f0 denovo2548_f0 denovo2574_f0 denovo2600_f0 denovo2626_f0 denovo2652_f0 denovo2756_f0 denovo2834_f0 denovo2886_f0 denovo3146_f0 denovo3250_f0 denovo3302_f0 denovo3328_f0 denovo3432_f0 denovo3484_f0 denovo3588_f0 denovo3614_f0 denovo3640_f0 denovo3718_f0 denovo3744_f0 denovo3796_f0 denovo3822_f0 denovo3978_f0 denovo4056_f0 denovo4134_f0 denovo4238_f0 denovo4316_f0 denovo4342_f0 denovo4368_f0 denovo4394_f0 denovo4420_f0 denovo4498_f0 denovo4524_f0 denovo4628_f0 denovo4758_f0 denovo4836_f0 denovo4888_f0 denovo4914_f0 denovo4940_f0 denovo4966_f0 denovo4992_f0 denovo5096_f0 denovo5148_f0 denovo5200_f0 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denovo9308_f0 denovo9334_f0 denovo9438_f0 denovo9464_f0 denovo9490_f0 denovo9646_f0 denovo9698_f0 denovo9776_f0 denovo9802_f0 denovo9828_f0 denovo9880_f0 denovo9958_f0 denovo10010_f0 denovo10036_f0 denovo10192_f0 denovo10218_f0 denovo10270_f0 denovo10296_f0 denovo10426_f0 denovo10452_f0 denovo10504_f0 denovo10530_f0 denovo10556_f0 denovo10582_f0 denovo10660_f0 denovo10712_f0 denovo10738_f0 denovo10764_f0 denovo10816_f0 denovo10998_f0 denovo11024_f0 denovo11050_f0 denovo11180_f0 denovo11284_f0 denovo11336_f0 denovo11388_f0 denovo11414_f0 denovo11440_f0 denovo11466_f0 denovo11492_f0 denovo11518_f0 denovo11570_f0 denovo11596_f0 denovo11700_f0 denovo11726_f0 denovo11908_f0 denovo11934_f0 denovo12064_f0 Pcit2 denovo19_f0 denovo97_f0 denovo175_f0 denovo201_f0 denovo279_f0 denovo331_f0 denovo383_f0 denovo461_f0 denovo539_f0 denovo695_f0 denovo851_f0 denovo1059_f0 denovo1163_f0 denovo1241_f0 denovo1267_f0 denovo1371_f0 denovo1397_f0 denovo1423_f0 denovo1501_f0 denovo1657_f0 denovo1683_f0 denovo1735_f0 denovo1813_f0 denovo1865_f0 denovo1943_f0 denovo1969_f0 denovo1995_f0 denovo2021_f0 denovo2099_f0 denovo2125_f0 denovo2151_f0 denovo2255_f0 denovo2281_f0 denovo2307_f0 denovo2333_f0 denovo2385_f0 denovo2489_f0 denovo2541_f0 denovo2567_f0 denovo2593_f0 denovo2619_f0 denovo2645_f0 denovo2671_f0 denovo2775_f0 denovo2853_f0 denovo2905_f0 denovo3165_f0 denovo3269_f0 denovo3321_f0 denovo3347_f0 denovo3451_f0 denovo3503_f0 denovo3607_f0 denovo3633_f0 denovo3659_f0 denovo3737_f0 denovo3763_f0 denovo3815_f0 denovo3841_f0 denovo3997_f0 denovo4075_f0 denovo4153_f0 denovo4257_f0 denovo4335_f0 denovo4361_f0 denovo4387_f0 denovo4413_f0 denovo4439_f0 denovo4517_f0 denovo4543_f0 denovo4647_f0 denovo4777_f0 denovo4855_f0 denovo4907_f0 denovo4933_f0 denovo4959_f0 denovo4985_f0 denovo5011_f0 denovo5115_f0 denovo5167_f0 denovo5219_f0 denovo5427_f0 denovo5453_f0 denovo5557_f0 denovo5583_f0 denovo5921_f0 denovo5973_f0 denovo6025_f0 denovo6051_f0 denovo6077_f0 denovo6103_f0 denovo6207_f0 denovo6259_f0 denovo6285_f0 denovo6311_f0 denovo6389_f0 denovo6519_f0 denovo6571_f0 denovo6597_f0 denovo6623_f0 denovo6675_f0 denovo6701_f0 denovo6727_f0 denovo6753_f0 denovo6779_f0 denovo6909_f0 denovo6987_f0 denovo7013_f0 denovo7039_f0 denovo7091_f0 denovo7143_f0 denovo7169_f0 denovo7299_f0 denovo7325_f0 denovo7351_f0 denovo7377_f0 denovo7403_f0 denovo7481_f0 denovo7507_f0 denovo7533_f0 denovo7559_f0 denovo7637_f0 denovo7689_f0 denovo7715_f0 denovo7793_f0 denovo7845_f0 denovo7923_f0 denovo8027_f0 denovo8053_f0 denovo8235_f0 denovo8261_f0 denovo8287_f0 denovo8365_f0 denovo8391_f0 denovo8417_f0 denovo8495_f0 denovo8547_f0 denovo8573_f0 denovo8625_f0 denovo8651_f0 denovo8703_f0 denovo8729_f0 denovo8755_f0 denovo8781_f0 denovo8911_f0 denovo8937_f0 denovo8963_f0 denovo8989_f0 denovo9119_f0 denovo9145_f0 denovo9249_f0 denovo9301_f0 denovo9327_f0 denovo9353_f0 denovo9457_f0 denovo9483_f0 denovo9509_f0 denovo9665_f0 denovo9717_f0 denovo9795_f0 denovo9821_f0 denovo9847_f0 denovo9899_f0 denovo9977_f0 denovo10029_f0 denovo10055_f0 denovo10211_f0 denovo10237_f0 denovo10289_f0 denovo10315_f0 denovo10445_f0 denovo10471_f0 denovo10523_f0 denovo10549_f0 denovo10575_f0 denovo10601_f0 denovo10679_f0 denovo10731_f0 denovo10757_f0 denovo10783_f0 denovo10835_f0 denovo11017_f0 denovo11043_f0 denovo11069_f0 denovo11199_f0 denovo11303_f0 denovo11355_f0 denovo11407_f0 denovo11433_f0 denovo11459_f0 denovo11485_f0 denovo11511_f0 denovo11537_f0 denovo11589_f0 denovo11615_f0 denovo11719_f0 denovo11745_f0 denovo11927_f0 denovo11953_f0 denovo12083_f0 Concatenation entropy_0.00_0.00_loci_150_to_349 will have the following data OTU EOG69CQC1_1 EOG69KFV8_1 EOG6SN1SH_1 EOG6PRSVJ_1 EOG6PRSVH_1 EOG60ZR1Z_1 EOG6FXRCN_1 EOG60P4BD_1 EOG6NCMGZ_1 EOG670TN2_1 EOG63TZZV_1 EOG6G7C30_1 EOG6K6G7Z_1 EOG6SXNH7_1 EOG65X80D_1 EOG68KRFS_1 EOG6MSD2X_1 EOG698V44_1 EOG6F7NPM_1 EOG676K3N_1 EOG6894QQ_1 EOG6868GW_1 EOG69PB31_1 EOG6JDHBD_1 EOG6C87X4_1 EOG68D102_1 EOG60ZR1T_1 EOG63JC89_1 EOG6J6RV9_1 EOG68D104_1 EOG68KRG8_1 EOG6N8R81_1 EOG63BMSV_1 EOG69KFV1_1 EOG6CJVMF_1 EOG6C2HF4_1 EOG6CC44S_1 EOG6FXRCK_1 EOG68KRG4_1 EOG61C70T_1 EOG6BK575_1 EOG6R506X_1 EOG6JT09G_1 EOG6HQDPG_1 EOG6H4677_1 EOG6SJ5J3_1 EOG6NZTZ3_1 EOG6J3WM7_1 EOG680J16_1 EOG602WWN_1 EOG6RNBCT_1 EOG63BMSB_1 EOG6B8JHB_1 EOG647FXX_1 EOG6B8JHP_1 EOG6S1TBX_1 EOG65HS25_1 EOG6FFD5C_1 EOG6PNXM9_1 EOG6F4SFZ_1 EOG6Q8524_1 EOG669QZR_1 EOG6JT09B_1 EOG6CJVMM_1 EOG6QRH81_1 EOG6NCMH9_1 EOG65HS1N_1 EOG6CC44T_1 EOG6FR0VW_1 EOG6KKZ6X_1 EOG60VVTG_1 EOG6QC198_1 EOG6FFD52_1 EOG634W9K_1 EOG6DNF7N_1 EOG61RPZF_1 EOG605S4X_1 EOG69GKMS_1 EOG6FR0VX_1 EOG6B8JHC_1 EOG6QVCGS_1 EOG6Q2DJZ_1 EOG6CC44M_1 EOG6NS3G8_1 EOG68GW77_1 EOG6229Q2_1 EOG63TZZW_1 EOG6MW89D_1 EOG6SJ5K0_1 EOG6MKNM3_1 EOG63V00H_1 EOG6BG90S_1 EOG66DM62_1 EOG69CQBW_1 EOG69KFTV_1 EOG62V8KS_1 EOG6FFD51_1 EOG6QNN0J_1 EOG6PC9WN_1 EOG6Q8529_1 EOG6KSPP5_1 EOG61ZFF6_1 EOG6N5W22_1 EOG63V009_1 EOG6PK2CG_1 EOG68GW6V_1 EOG66Q6XP_1 EOG6C5CNP_1 EOG6R5066_1 EOG641QFN_1 EOG65B1K2_1 EOG65TCRK_1 EOG6PNXN7_1 EOG6P2Q64_1 EOG666VQC_1 EOG6PC9WF_1 EOG6Q58T0_1 EOG641QGH_1 EOG6933N7_1 EOG69S6BG_1 EOG66Q6XR_1 EOG6PK2CM_1 EOG6NS3FV_1 EOG641QFW_1 EOG6N04J6_1 EOG6CRM3G_1 EOG6S4PKX_1 EOG6K6G7S_1 EOG6BZN62_1 EOG68SGZ1_1 EOG6SXNGX_1 EOG6QZ7Q8_1 EOG6QC18P_1 EOG6CG0CT_1 EOG6PK2CQ_1 EOG6JWVJQ_1 EOG6PG64S_1 EOG63R3RK_1 EOG64F6DK_1 EOG6FJ8D6_1 EOG6001NN_1 EOG695ZWC_1 EOG67PX9B_1 EOG6P8FNH_1 EOG6KSPQ0_1 EOG63R3RC_1 EOG6907D7_1 EOG6JWVHT_1 EOG68SGX8_1 EOG6933NR_1 EOG62JNVR_1 EOG64MXWZ_1 EOG6S1TC2_1 EOG6PC9X3_1 EOG6Q58SW_1 EOG6CRM3H_1 EOG6R5069_1 EOG64MXWK_1 EOG6N30SN_1 EOG68KRFQ_1 EOG6DR9GZ_1 EOG62FSN7_1 EOG6PZJB1_1 EOG65QHHP_1 EOG615GHV_1 EOG66WZCQ_1 EOG698V4H_1 EOG6JDHB2_1 EOG62BXCX_1 EOG69KFVF_1 EOG615GHP_1 EOG66HGF5_1 EOG6DFPSF_1 EOG66MBPR_1 EOG6DFPSD_1 EOG67D9KC_1 EOG6HHP5S_1 EOG6DBTHZ_1 EOG6KH2ZD_1 EOG6STS87_1 EOG67D9KV_1 EOG65MN8T_1 EOG61RPZ9_1 EOG66MBP7_1 EOG6QJRRQ_1 EOG6Q852B_1 EOG6DV5QM_1 EOG6K0QRT_1 EOG65DWSM_1 EOG6G4GTX_1 EOG64BB5H_1 EOG64J2NC_1 EOG6H72G3_1 EOG6SBF2B_1 EOG6FFD5V_1 EOG6G4GTT_1 EOG6K3M11_1 EOG66147J_1 EOG63FH1C_1 EOG61C70W_1 Dplexcds denovo2_f0 denovo54_f0 denovo80_f0 denovo158_f0 denovo184_f0 denovo262_f0 denovo314_f0 denovo366_f0 denovo444_f0 denovo548_f0 denovo678_f0 denovo834_f0 denovo860_f0 denovo886_f0 denovo912_f0 denovo1042_f0 denovo1172_f0 denovo1224_f0 denovo1250_f0 denovo1276_f0 denovo1354_f0 denovo1380_f0 denovo1406_f0 denovo1484_f0 denovo1562_f0 denovo1640_f0 denovo1666_f0 denovo1718_f0 denovo1848_f0 denovo1900_f0 denovo1926_f0 denovo1952_f0 denovo1978_f0 denovo2004_f0 denovo2056_f0 denovo2082_f0 denovo2108_f0 denovo2134_f0 denovo2238_f0 denovo2264_f0 denovo2290_f0 denovo2316_f0 denovo2368_f0 denovo2394_f0 denovo2420_f0 denovo2550_f0 denovo2576_f0 denovo2602_f0 denovo2628_f0 denovo2732_f0 denovo2758_f0 denovo2810_f0 denovo2888_f0 denovo3304_f0 denovo3330_f0 denovo3434_f0 denovo3590_f0 denovo3616_f0 denovo3642_f0 denovo3720_f0 denovo3746_f0 denovo3798_f0 denovo3824_f0 denovo3876_f0 denovo4058_f0 denovo4084_f0 denovo4136_f0 denovo4162_f0 denovo4240_f0 denovo4318_f0 denovo4344_f0 denovo4370_f0 denovo4422_f0 denovo4500_f0 denovo4526_f0 denovo4630_f0 denovo4838_f0 denovo4994_f0 denovo5020_f0 denovo5098_f0 denovo5124_f0 denovo5150_f0 denovo5332_f0 denovo5410_f0 denovo5488_f0 denovo5540_f0 denovo5566_f0 denovo5722_f0 denovo5774_f0 denovo5852_f0 denovo5878_f0 denovo5904_f0 denovo5956_f0 denovo6034_f0 denovo6086_f0 denovo6190_f0 denovo6268_f0 denovo6294_f0 denovo6320_f0 denovo6346_f0 denovo6372_f0 denovo6476_f0 denovo6502_f0 denovo6528_f0 denovo6554_f0 denovo6632_f0 denovo6658_f0 denovo6710_f0 denovo6736_f0 denovo6892_f0 denovo6970_f0 denovo7022_f0 denovo7048_f0 denovo7126_f0 denovo7152_f0 denovo7282_f0 denovo7308_f0 denovo7334_f0 denovo7360_f0 denovo7386_f0 denovo7438_f0 denovo7464_f0 denovo7490_f0 denovo7542_f0 denovo7620_f0 denovo7646_f0 denovo7698_f0 denovo7776_f0 denovo7828_f0 denovo7854_f0 denovo7906_f0 denovo7932_f0 denovo8010_f0 denovo8036_f0 denovo8088_f0 denovo8140_f0 denovo8192_f0 denovo8348_f0 denovo8374_f0 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denovo4101_f0 denovo4153_f0 denovo4179_f0 denovo4257_f0 denovo4335_f0 denovo4361_f0 denovo4387_f0 denovo4439_f0 denovo4517_f0 denovo4543_f0 denovo4647_f0 denovo4855_f0 denovo5011_f0 denovo5037_f0 denovo5115_f0 denovo5141_f0 denovo5167_f0 denovo5349_f0 denovo5427_f0 denovo5505_f0 denovo5557_f0 denovo5583_f0 denovo5739_f0 denovo5791_f0 denovo5869_f0 denovo5895_f0 denovo5921_f0 denovo5973_f0 denovo6051_f0 denovo6103_f0 denovo6207_f0 denovo6285_f0 denovo6311_f0 denovo6337_f0 denovo6363_f0 denovo6389_f0 denovo6493_f0 denovo6519_f0 denovo6545_f0 denovo6571_f0 denovo6649_f0 denovo6675_f0 denovo6727_f0 denovo6753_f0 denovo6909_f0 denovo6987_f0 denovo7039_f0 denovo7065_f0 denovo7143_f0 denovo7169_f0 denovo7299_f0 denovo7325_f0 denovo7351_f0 denovo7377_f0 denovo7403_f0 denovo7455_f0 denovo7481_f0 denovo7507_f0 denovo7559_f0 denovo7637_f0 denovo7663_f0 denovo7715_f0 denovo7793_f0 denovo7845_f0 denovo7871_f0 denovo7923_f0 denovo7949_f0 denovo8027_f0 denovo8053_f0 denovo8105_f0 denovo8157_f0 denovo8209_f0 denovo8365_f0 denovo8391_f0 denovo8417_f0 denovo8495_f0 denovo8547_f0 denovo8573_f0 denovo8625_f0 denovo8651_f0 denovo8703_f0 denovo8729_f0 denovo8755_f0 denovo8781_f0 denovo9067_f0 denovo9093_f0 denovo9119_f0 denovo9145_f0 denovo9223_f0 denovo9249_f0 denovo9301_f0 denovo9353_f0 denovo9483_f0 denovo9509_f0 denovo9639_f0 denovo9665_f0 denovo9795_f0 denovo9847_f0 denovo9899_f0 denovo9977_f0 denovo10029_f0 denovo10055_f0 denovo10133_f0 denovo10159_f0 denovo10289_f0 denovo10315_f0 denovo10445_f0 denovo10471_f0 denovo10523_f0 denovo10549_f0 denovo10575_f0 denovo10601_f0 denovo10731_f0 denovo10757_f0 denovo10783_f0 denovo10835_f0 denovo10913_f0 denovo11017_f0 denovo11069_f0 denovo11147_f0 denovo11225_f0 denovo11303_f0 denovo11407_f0 denovo11433_f0 denovo11485_f0 denovo11511_f0 denovo11537_f0 denovo11589_f0 denovo11615_f0 denovo11719_f0 denovo11745_f0 denovo11771_f0 denovo11875_f0 denovo11901_f0 denovo11953_f0 Concatenation entropy_0.00_0.00_loci_200_to_399 will have the following data OTU EOG69CQC1_1 EOG69KFV8_1 EOG6PRSVJ_1 EOG6PRSVH_1 EOG6FXRCN_1 EOG60P4BD_1 EOG6BCDR6_1 EOG6NCMGZ_1 EOG67SSJD_1 EOG670TN2_1 EOG647FZH_1 EOG6D5327_1 EOG63TZZV_1 EOG6HDSZD_1 EOG68WC5N_1 EOG68SGXD_1 EOG6G7C30_1 EOG6K6G7Z_1 EOG6SXNH7_1 EOG65X80D_1 EOG6SJ5J4_1 EOG6C87X0_1 EOG65493R_1 EOG6868HF_1 EOG6MSD2X_1 EOG63FH1T_1 EOG698V44_1 EOG6F7NPM_1 EOG676K3N_1 EOG6KWJXS_1 EOG6894QQ_1 EOG6868GW_1 EOG69PB31_1 EOG6SJ5JV_1 EOG65492X_1 EOG67H5VB_1 EOG6C87X4_1 EOG61C717_1 EOG673PVJ_1 EOG60ZR1T_1 EOG68WC5K_1 EOG63JC89_1 EOG6GHZSZ_1 EOG6J6RV9_1 EOG6S4PM1_1 EOG68D104_1 EOG68KRG8_1 EOG63BMSV_1 EOG69KFV1_1 EOG6H1B0Q_1 EOG6CJVMF_1 EOG6C2HF4_1 EOG6CC44S_1 EOG6M65N3_1 EOG6BK57N_1 EOG6BK575_1 EOG6R506X_1 EOG6JT09G_1 EOG6HQDPG_1 EOG6H4677_1 EOG6SJ5J3_1 EOG680J16_1 EOG60K843_1 EOG65X811_1 EOG602WWN_1 EOG63BMSB_1 EOG6B8JHB_1 EOG654930_1 EOG6PVP2X_1 EOG6RXZ3G_1 EOG602WX4_1 EOG6KH2ZX_1 EOG61JZGH_1 EOG6SJ5J9_1 EOG6STS8H_1 EOG6F7NPN_1 EOG6GHZSG_1 EOG6P8FN9_1 EOG6R506R_1 EOG65TCRW_1 EOG6HX54P_1 EOG60VVST_1 EOG6PNXM9_1 EOG6Q8524_1 EOG669QZR_1 EOG6JT09B_1 EOG6CJVMM_1 EOG6K9BH5_1 EOG63N7HX_1 EOG6JQ426_1 EOG6NCMH9_1 EOG6FN4N0_1 EOG65HS1N_1 EOG6CC44T_1 EOG6K9BGH_1 EOG6FR0VW_1 EOG6N8R82_1 EOG6QC198_1 EOG6FFD52_1 EOG6KKZ71_1 EOG634W9K_1 EOG6DNF7N_1 EOG6BG909_1 EOG63BMSG_1 EOG6FR0VX_1 EOG6B8JHC_1 EOG6QVCGS_1 EOG6Q2DJZ_1 EOG6CC44M_1 EOG6NS3G8_1 EOG68GW77_1 EOG6229Q2_1 EOG63TZZW_1 EOG6MW89D_1 EOG6SJ5K0_1 EOG6MKNM3_1 EOG63V00H_1 EOG6BG90S_1 EOG66DM62_1 EOG69CQBW_1 EOG69KFTV_1 EOG62V8KS_1 EOG6QNN0J_1 EOG6PC9WN_1 EOG6Q8529_1 EOG6KSPP5_1 EOG61ZFF6_1 EOG6N5W22_1 EOG63V009_1 EOG6PK2CG_1 EOG68GW6V_1 EOG66Q6XP_1 EOG6R5066_1 EOG641QFN_1 EOG65B1K2_1 EOG65TCRK_1 EOG6PNXN7_1 EOG6PC9WF_1 EOG6Q58T0_1 EOG6933N7_1 EOG66Q6XR_1 EOG6PK2CM_1 EOG6NS3FV_1 EOG6CRM3G_1 EOG6K6G7S_1 EOG6BZN62_1 EOG68SGZ1_1 EOG6SXNGX_1 EOG6QZ7Q8_1 EOG6QC18P_1 EOG6PK2CQ_1 EOG6JWVJQ_1 EOG6PG64S_1 EOG63R3RK_1 EOG64F6DK_1 EOG6001NN_1 EOG695ZWC_1 EOG67PX9B_1 EOG6P8FNH_1 EOG6907D7_1 EOG6JWVHT_1 EOG6933NR_1 EOG62JNVR_1 EOG64MXWZ_1 EOG6PC9X3_1 EOG6Q58SW_1 EOG6CRM3H_1 EOG64MXWK_1 EOG68KRFQ_1 EOG6DR9GZ_1 EOG62FSN7_1 EOG66WZCQ_1 EOG698V4H_1 EOG6JDHB2_1 EOG62BXCX_1 EOG6DFPSF_1 EOG67D9KC_1 EOG6HHP5S_1 EOG6DBTHZ_1 EOG6KH2ZD_1 EOG67D9KV_1 EOG65MN8T_1 EOG61RPZ9_1 EOG66MBP7_1 EOG6QJRRQ_1 EOG6Q852B_1 EOG6DV5QM_1 EOG6K0QRT_1 EOG65DWSM_1 EOG6G4GTX_1 EOG64BB5H_1 EOG64J2NC_1 EOG6H72G3_1 EOG6SBF2B_1 EOG6FFD5V_1 EOG6G4GTT_1 EOG6K3M11_1 EOG66147J_1 EOG63FH1C_1 EOG61C70W_1 Dplexcds denovo2_f0 denovo54_f0 denovo158_f0 denovo184_f0 denovo314_f0 denovo366_f0 denovo392_f0 denovo444_f0 denovo496_f0 denovo548_f0 denovo626_f0 denovo652_f0 denovo678_f0 denovo704_f0 denovo756_f0 denovo808_f0 denovo834_f0 denovo860_f0 denovo886_f0 denovo912_f0 denovo990_f0 denovo1016_f0 denovo1094_f0 denovo1120_f0 denovo1172_f0 denovo1198_f0 denovo1224_f0 denovo1250_f0 denovo1276_f0 denovo1328_f0 denovo1354_f0 denovo1380_f0 denovo1406_f0 denovo1432_f0 denovo1458_f0 denovo1536_f0 denovo1562_f0 denovo1588_f0 denovo1614_f0 denovo1666_f0 denovo1692_f0 denovo1718_f0 denovo1822_f0 denovo1848_f0 denovo1874_f0 denovo1900_f0 denovo1926_f0 denovo1978_f0 denovo2004_f0 denovo2030_f0 denovo2056_f0 denovo2082_f0 denovo2108_f0 denovo2160_f0 denovo2212_f0 denovo2290_f0 denovo2316_f0 denovo2368_f0 denovo2394_f0 denovo2420_f0 denovo2550_f0 denovo2628_f0 denovo2680_f0 denovo2706_f0 denovo2732_f0 denovo2810_f0 denovo2888_f0 denovo2940_f0 denovo2966_f0 denovo3018_f0 denovo3070_f0 denovo3096_f0 denovo3122_f0 denovo3174_f0 denovo3200_f0 denovo3356_f0 denovo3382_f0 denovo3408_f0 denovo3460_f0 denovo3512_f0 denovo3538_f0 denovo3564_f0 denovo3642_f0 denovo3746_f0 denovo3798_f0 denovo3824_f0 denovo3876_f0 denovo3902_f0 denovo3928_f0 denovo4006_f0 denovo4084_f0 denovo4110_f0 denovo4136_f0 denovo4162_f0 denovo4214_f0 denovo4240_f0 denovo4266_f0 denovo4370_f0 denovo4422_f0 denovo4474_f0 denovo4500_f0 denovo4526_f0 denovo4578_f0 denovo4604_f0 denovo5020_f0 denovo5098_f0 denovo5124_f0 denovo5150_f0 denovo5332_f0 denovo5410_f0 denovo5488_f0 denovo5540_f0 denovo5566_f0 denovo5722_f0 denovo5774_f0 denovo5852_f0 denovo5878_f0 denovo5904_f0 denovo5956_f0 denovo6034_f0 denovo6086_f0 denovo6190_f0 denovo6294_f0 denovo6320_f0 denovo6346_f0 denovo6372_f0 denovo6476_f0 denovo6502_f0 denovo6528_f0 denovo6554_f0 denovo6632_f0 denovo6658_f0 denovo6736_f0 denovo6892_f0 denovo6970_f0 denovo7022_f0 denovo7048_f0 denovo7282_f0 denovo7308_f0 denovo7360_f0 denovo7438_f0 denovo7464_f0 denovo7490_f0 denovo7646_f0 denovo7776_f0 denovo7828_f0 denovo7854_f0 denovo7906_f0 denovo7932_f0 denovo8010_f0 denovo8088_f0 denovo8140_f0 denovo8192_f0 denovo8348_f0 denovo8374_f0 denovo8478_f0 denovo8530_f0 denovo8556_f0 denovo8608_f0 denovo8712_f0 denovo8738_f0 denovo9050_f0 denovo9076_f0 denovo9102_f0 denovo9206_f0 denovo9232_f0 denovo9284_f0 denovo9466_f0 denovo9622_f0 denovo9648_f0 denovo9778_f0 denovo10012_f0 denovo10038_f0 denovo10116_f0 denovo10142_f0 denovo10454_f0 denovo10558_f0 denovo10584_f0 denovo10714_f0 denovo10740_f0 denovo10818_f0 denovo10896_f0 denovo11000_f0 denovo11052_f0 denovo11130_f0 denovo11208_f0 denovo11286_f0 denovo11390_f0 denovo11416_f0 denovo11468_f0 denovo11494_f0 denovo11520_f0 denovo11572_f0 denovo11598_f0 denovo11702_f0 denovo11728_f0 denovo11754_f0 denovo11858_f0 denovo11884_f0 denovo11936_f0 FG120077 denovo10_f0 denovo62_f0 denovo166_f0 denovo192_f0 denovo322_f0 denovo374_f0 denovo400_f0 denovo452_f0 denovo504_f0 denovo556_f0 denovo634_f0 denovo660_f0 denovo686_f0 denovo712_f0 denovo764_f0 denovo816_f0 denovo842_f0 denovo868_f0 denovo894_f0 denovo920_f0 denovo998_f0 denovo1024_f0 denovo1102_f0 denovo1128_f0 denovo1180_f0 denovo1206_f0 denovo1232_f0 denovo1258_f0 denovo1284_f0 denovo1336_f0 denovo1362_f0 denovo1388_f0 denovo1414_f0 denovo1440_f0 denovo1466_f0 denovo1544_f0 denovo1570_f0 denovo1596_f0 denovo1622_f0 denovo1674_f0 denovo1700_f0 denovo1726_f0 denovo1830_f0 denovo1856_f0 denovo1882_f0 denovo1908_f0 denovo1934_f0 denovo1986_f0 denovo2012_f0 denovo2038_f0 denovo2064_f0 denovo2090_f0 denovo2116_f0 denovo2168_f0 denovo2220_f0 denovo2298_f0 denovo2324_f0 denovo2376_f0 denovo2402_f0 denovo2428_f0 denovo2558_f0 denovo2636_f0 denovo2688_f0 denovo2714_f0 denovo2740_f0 denovo2818_f0 denovo2896_f0 denovo2948_f0 denovo2974_f0 denovo3026_f0 denovo3078_f0 denovo3104_f0 denovo3130_f0 denovo3182_f0 denovo3208_f0 denovo3364_f0 denovo3390_f0 denovo3416_f0 denovo3468_f0 denovo3520_f0 denovo3546_f0 denovo3572_f0 denovo3650_f0 denovo3754_f0 denovo3806_f0 denovo3832_f0 denovo3884_f0 denovo3910_f0 denovo3936_f0 denovo4014_f0 denovo4092_f0 denovo4118_f0 denovo4144_f0 denovo4170_f0 denovo4222_f0 denovo4248_f0 denovo4274_f0 denovo4378_f0 denovo4430_f0 denovo4482_f0 denovo4508_f0 denovo4534_f0 denovo4586_f0 denovo4612_f0 denovo5028_f0 denovo5106_f0 denovo5132_f0 denovo5158_f0 denovo5340_f0 denovo5418_f0 denovo5496_f0 denovo5548_f0 denovo5574_f0 denovo5730_f0 denovo5782_f0 denovo5860_f0 denovo5886_f0 denovo5912_f0 denovo5964_f0 denovo6042_f0 denovo6094_f0 denovo6198_f0 denovo6302_f0 denovo6328_f0 denovo6354_f0 denovo6380_f0 denovo6484_f0 denovo6510_f0 denovo6536_f0 denovo6562_f0 denovo6640_f0 denovo6666_f0 denovo6744_f0 denovo6900_f0 denovo6978_f0 denovo7030_f0 denovo7056_f0 denovo7290_f0 denovo7316_f0 denovo7368_f0 denovo7446_f0 denovo7472_f0 denovo7498_f0 denovo7654_f0 denovo7784_f0 denovo7836_f0 denovo7862_f0 denovo7914_f0 denovo7940_f0 denovo8018_f0 denovo8096_f0 denovo8148_f0 denovo8200_f0 denovo8356_f0 denovo8382_f0 denovo8486_f0 denovo8538_f0 denovo8564_f0 denovo8616_f0 denovo8720_f0 denovo8746_f0 denovo9058_f0 denovo9084_f0 denovo9110_f0 denovo9214_f0 denovo9240_f0 denovo9292_f0 denovo9474_f0 denovo9630_f0 denovo9656_f0 denovo9786_f0 denovo10020_f0 denovo10046_f0 denovo10124_f0 denovo10150_f0 denovo10462_f0 denovo10566_f0 denovo10592_f0 denovo10722_f0 denovo10748_f0 denovo10826_f0 denovo10904_f0 denovo11008_f0 denovo11060_f0 denovo11138_f0 denovo11216_f0 denovo11294_f0 denovo11398_f0 denovo11424_f0 denovo11476_f0 denovo11502_f0 denovo11528_f0 denovo11580_f0 denovo11606_f0 denovo11710_f0 denovo11736_f0 denovo11762_f0 denovo11866_f0 denovo11892_f0 denovo11944_f0 SRR803483 denovo20_f0 denovo72_f0 denovo176_f0 denovo202_f0 denovo332_f0 denovo384_f0 denovo410_f0 denovo462_f0 denovo514_f0 denovo566_f0 denovo644_f0 denovo670_f0 denovo696_f0 denovo722_f0 denovo774_f0 denovo826_f0 denovo852_f0 denovo878_f0 denovo904_f0 denovo930_f0 denovo1008_f0 denovo1034_f0 denovo1112_f0 denovo1138_f0 denovo1190_f0 denovo1216_f0 denovo1242_f0 denovo1268_f0 denovo1294_f0 denovo1346_f0 denovo1372_f0 denovo1398_f0 denovo1424_f0 denovo1450_f0 denovo1476_f0 denovo1554_f0 denovo1580_f0 denovo1606_f0 denovo1632_f0 denovo1684_f0 denovo1710_f0 denovo1736_f0 denovo1840_f0 denovo1866_f0 denovo1892_f0 denovo1918_f0 denovo1944_f0 denovo1996_f0 denovo2022_f0 denovo2048_f0 denovo2074_f0 denovo2100_f0 denovo2126_f0 denovo2178_f0 denovo2230_f0 denovo2308_f0 denovo2334_f0 denovo2386_f0 denovo2412_f0 denovo2438_f0 denovo2568_f0 denovo2646_f0 denovo2698_f0 denovo2724_f0 denovo2750_f0 denovo2828_f0 denovo2906_f0 denovo2958_f0 denovo2984_f0 denovo3036_f0 denovo3088_f0 denovo3114_f0 denovo3140_f0 denovo3192_f0 denovo3218_f0 denovo3374_f0 denovo3400_f0 denovo3426_f0 denovo3478_f0 denovo3530_f0 denovo3556_f0 denovo3582_f0 denovo3660_f0 denovo3764_f0 denovo3816_f0 denovo3842_f0 denovo3894_f0 denovo3920_f0 denovo3946_f0 denovo4024_f0 denovo4102_f0 denovo4128_f0 denovo4154_f0 denovo4180_f0 denovo4232_f0 denovo4258_f0 denovo4284_f0 denovo4388_f0 denovo4440_f0 denovo4492_f0 denovo4518_f0 denovo4544_f0 denovo4596_f0 denovo4622_f0 denovo5038_f0 denovo5116_f0 denovo5142_f0 denovo5168_f0 denovo5350_f0 denovo5428_f0 denovo5506_f0 denovo5558_f0 denovo5584_f0 denovo5740_f0 denovo5792_f0 denovo5870_f0 denovo5896_f0 denovo5922_f0 denovo5974_f0 denovo6052_f0 denovo6104_f0 denovo6208_f0 denovo6312_f0 denovo6338_f0 denovo6364_f0 denovo6390_f0 denovo6494_f0 denovo6520_f0 denovo6546_f0 denovo6572_f0 denovo6650_f0 denovo6676_f0 denovo6754_f0 denovo6910_f0 denovo6988_f0 denovo7040_f0 denovo7066_f0 denovo7300_f0 denovo7326_f0 denovo7378_f0 denovo7456_f0 denovo7482_f0 denovo7508_f0 denovo7664_f0 denovo7794_f0 denovo7846_f0 denovo7872_f0 denovo7924_f0 denovo7950_f0 denovo8028_f0 denovo8106_f0 denovo8158_f0 denovo8210_f0 denovo8366_f0 denovo8392_f0 denovo8496_f0 denovo8548_f0 denovo8574_f0 denovo8626_f0 denovo8730_f0 denovo8756_f0 denovo9068_f0 denovo9094_f0 denovo9120_f0 denovo9224_f0 denovo9250_f0 denovo9302_f0 denovo9484_f0 denovo9640_f0 denovo9666_f0 denovo9796_f0 denovo10030_f0 denovo10056_f0 denovo10134_f0 denovo10160_f0 denovo10472_f0 denovo10576_f0 denovo10602_f0 denovo10732_f0 denovo10758_f0 denovo10836_f0 denovo10914_f0 denovo11018_f0 denovo11070_f0 denovo11148_f0 denovo11226_f0 denovo11304_f0 denovo11408_f0 denovo11434_f0 denovo11486_f0 denovo11512_f0 denovo11538_f0 denovo11590_f0 denovo11616_f0 denovo11720_f0 denovo11746_f0 denovo11772_f0 denovo11876_f0 denovo11902_f0 denovo11954_f0 FG120035 denovo5_f0 denovo57_f0 denovo161_f0 denovo187_f0 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denovo5772_f0 denovo5850_f0 denovo5876_f0 denovo5902_f0 denovo5954_f0 denovo6032_f0 denovo6084_f0 denovo6188_f0 denovo6292_f0 denovo6318_f0 denovo6344_f0 denovo6370_f0 denovo6474_f0 denovo6500_f0 denovo6526_f0 denovo6552_f0 denovo6630_f0 denovo6656_f0 denovo6734_f0 denovo6890_f0 denovo6968_f0 denovo7020_f0 denovo7046_f0 denovo7280_f0 denovo7306_f0 denovo7358_f0 denovo7436_f0 denovo7462_f0 denovo7488_f0 denovo7644_f0 denovo7774_f0 denovo7826_f0 denovo7852_f0 denovo7904_f0 denovo7930_f0 denovo8008_f0 denovo8086_f0 denovo8138_f0 denovo8190_f0 denovo8346_f0 denovo8372_f0 denovo8476_f0 denovo8528_f0 denovo8554_f0 denovo8606_f0 denovo8710_f0 denovo8736_f0 denovo9048_f0 denovo9074_f0 denovo9100_f0 denovo9204_f0 denovo9230_f0 denovo9282_f0 denovo9464_f0 denovo9620_f0 denovo9646_f0 denovo9776_f0 denovo10010_f0 denovo10036_f0 denovo10114_f0 denovo10140_f0 denovo10452_f0 denovo10556_f0 denovo10582_f0 denovo10712_f0 denovo10738_f0 denovo10816_f0 denovo10894_f0 denovo10998_f0 denovo11050_f0 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denovo2307_f0 denovo2333_f0 denovo2385_f0 denovo2411_f0 denovo2437_f0 denovo2567_f0 denovo2645_f0 denovo2697_f0 denovo2723_f0 denovo2749_f0 denovo2827_f0 denovo2905_f0 denovo2957_f0 denovo2983_f0 denovo3035_f0 denovo3087_f0 denovo3113_f0 denovo3139_f0 denovo3191_f0 denovo3217_f0 denovo3373_f0 denovo3399_f0 denovo3425_f0 denovo3477_f0 denovo3529_f0 denovo3555_f0 denovo3581_f0 denovo3659_f0 denovo3763_f0 denovo3815_f0 denovo3841_f0 denovo3893_f0 denovo3919_f0 denovo3945_f0 denovo4023_f0 denovo4101_f0 denovo4127_f0 denovo4153_f0 denovo4179_f0 denovo4231_f0 denovo4257_f0 denovo4283_f0 denovo4387_f0 denovo4439_f0 denovo4491_f0 denovo4517_f0 denovo4543_f0 denovo4595_f0 denovo4621_f0 denovo5037_f0 denovo5115_f0 denovo5141_f0 denovo5167_f0 denovo5349_f0 denovo5427_f0 denovo5505_f0 denovo5557_f0 denovo5583_f0 denovo5739_f0 denovo5791_f0 denovo5869_f0 denovo5895_f0 denovo5921_f0 denovo5973_f0 denovo6051_f0 denovo6103_f0 denovo6207_f0 denovo6311_f0 denovo6337_f0 denovo6363_f0 denovo6389_f0 denovo6493_f0 denovo6519_f0 denovo6545_f0 denovo6571_f0 denovo6649_f0 denovo6675_f0 denovo6753_f0 denovo6909_f0 denovo6987_f0 denovo7039_f0 denovo7065_f0 denovo7299_f0 denovo7325_f0 denovo7377_f0 denovo7455_f0 denovo7481_f0 denovo7507_f0 denovo7663_f0 denovo7793_f0 denovo7845_f0 denovo7871_f0 denovo7923_f0 denovo7949_f0 denovo8027_f0 denovo8105_f0 denovo8157_f0 denovo8209_f0 denovo8365_f0 denovo8391_f0 denovo8495_f0 denovo8547_f0 denovo8573_f0 denovo8625_f0 denovo8729_f0 denovo8755_f0 denovo9067_f0 denovo9093_f0 denovo9119_f0 denovo9223_f0 denovo9249_f0 denovo9301_f0 denovo9483_f0 denovo9639_f0 denovo9665_f0 denovo9795_f0 denovo10029_f0 denovo10055_f0 denovo10133_f0 denovo10159_f0 denovo10471_f0 denovo10575_f0 denovo10601_f0 denovo10731_f0 denovo10757_f0 denovo10835_f0 denovo10913_f0 denovo11017_f0 denovo11069_f0 denovo11147_f0 denovo11225_f0 denovo11303_f0 denovo11407_f0 denovo11433_f0 denovo11485_f0 denovo11511_f0 denovo11537_f0 denovo11589_f0 denovo11615_f0 denovo11719_f0 denovo11745_f0 denovo11771_f0 denovo11875_f0 denovo11901_f0 denovo11953_f0 Concatenation entropy_0.00_0.00_loci_250_to_449 will have the following data OTU EOG69KFV8_1 EOG6PRSVH_1 EOG6FXRCN_1 EOG6BCDR6_1 EOG67SSJD_1 EOG670TN2_1 EOG647FZH_1 EOG6D5327_1 EOG63TZZV_1 EOG6HDSZD_1 EOG68WC5N_1 EOG68SGXD_1 EOG6G7C30_1 EOG6K6G7Z_1 EOG6SXNH7_1 EOG65X80D_1 EOG6SJ5J4_1 EOG6C87X0_1 EOG65493R_1 EOG6868HF_1 EOG6MSD2X_1 EOG63FH1T_1 EOG6F7NPM_1 EOG676K3N_1 EOG6KWJXS_1 EOG6SJ5JV_1 EOG65492X_1 EOG67H5VB_1 EOG6C87X4_1 EOG61C717_1 EOG673PVJ_1 EOG68WC5K_1 EOG63JC89_1 EOG6GHZSZ_1 EOG6J6RV9_1 EOG6S4PM1_1 EOG68D104_1 EOG6H1B0Q_1 EOG6CJVMF_1 EOG6C2HF4_1 EOG6M65N3_1 EOG6BK57N_1 EOG6R506X_1 EOG6JT09G_1 EOG6HQDPG_1 EOG6H4677_1 EOG6SJ5J3_1 EOG60K843_1 EOG65X811_1 EOG602WWN_1 EOG63BMSB_1 EOG6B8JHB_1 EOG654930_1 EOG6PVP2X_1 EOG6RXZ3G_1 EOG602WX4_1 EOG6KH2ZX_1 EOG61JZGH_1 EOG6SJ5J9_1 EOG6STS8H_1 EOG6F7NPN_1 EOG6GHZSG_1 EOG6P8FN9_1 EOG6R506R_1 EOG65TCRW_1 EOG6HX54P_1 EOG60VVST_1 EOG6PNXM9_1 EOG6CJVMM_1 EOG6K9BH5_1 EOG63N7HX_1 EOG6JQ426_1 EOG6NCMH9_1 EOG6FN4N0_1 EOG65HS1N_1 EOG6CC44T_1 EOG6K9BGH_1 EOG6FR0VW_1 EOG6N8R82_1 EOG6FFD52_1 EOG6KKZ71_1 EOG634W9K_1 EOG6DNF7N_1 EOG6BG909_1 EOG63BMSG_1 EOG6BVRZ3_1 EOG6MSD3H_1 EOG60CHM6_1 EOG66MBNX_1 EOG66HGF2_1 EOG6FR0VX_1 EOG6P2Q5K_1 EOG634W9M_1 EOG6B8JHC_1 EOG6QVCGS_1 EOG6Q2DJZ_1 EOG64TPC4_1 EOG6DNF8K_1 EOG68GW71_1 EOG6CC44M_1 EOG63JC8S_1 EOG6NS3G8_1 EOG6PNXM6_1 EOG68GW77_1 EOG6229Q2_1 EOG63TZZW_1 EOG63R3QZ_1 EOG65QHJ5_1 EOG6MW89D_1 EOG64F6DH_1 EOG6SJ5K0_1 EOG69GKM6_1 EOG66HGFW_1 EOG6MKNM3_1 EOG63V00H_1 EOG6BG90S_1 EOG6JQ41Z_1 EOG69CQBW_1 EOG6SBF24_1 EOG6P8FNB_1 EOG6PC9WN_1 EOG6Q8529_1 EOG6G1MMG_1 EOG63XV6Q_1 EOG6D531X_1 EOG61ZFF6_1 EOG63V009_1 EOG68GW6V_1 EOG6GXFRF_1 EOG6KWJX8_1 EOG641QFN_1 EOG6S1TBT_1 EOG6GB79M_1 EOG65TCRK_1 EOG6PNXN7_1 EOG6QRH78_1 EOG6FJ8F2_1 EOG6HHP6H_1 EOG6DJK1Q_1 EOG66Q6XR_1 EOG6PK2CM_1 EOG6DZ1ZZ_1 EOG6CRM3G_1 EOG65MN9F_1 EOG6K6G7S_1 EOG68SGZ1_1 EOG69PB2Z_1 EOG6QZ7Q8_1 EOG6DR9GP_1 EOG6QC18P_1 EOG6PK2CQ_1 EOG67D9KJ_1 EOG6JWVJQ_1 EOG6F1X6H_1 EOG6PG64S_1 EOG6B5P96_1 EOG63R3RK_1 EOG6001NN_1 EOG62V8KH_1 EOG695ZWC_1 EOG6P8FNH_1 EOG6907D7_1 EOG6JWVHT_1 EOG6HDSZ9_1 EOG6SXNHD_1 EOG6Q58ST_1 EOG6933NR_1 EOG62JNVR_1 EOG64MXWZ_1 EOG6PC9X3_1 EOG6Q58SW_1 EOG63N7HF_1 EOG63BMS7_1 EOG64MXWK_1 EOG6575BP_1 EOG615GJK_1 EOG68KRFQ_1 EOG6DR9GZ_1 EOG6PG646_1 EOG6C87WM_1 EOG66WZCQ_1 EOG698V4H_1 EOG6001NK_1 EOG6JDHB2_1 EOG62BXCX_1 EOG6JM7SX_1 EOG67D9KC_1 EOG6HHP5S_1 EOG65MN8T_1 EOG66MBP7_1 EOG6QJRRQ_1 EOG6Q852B_1 EOG64BB5H_1 EOG64J2NC_1 EOG6H72G3_1 EOG6SBF2B_1 EOG6K3M11_1 EOG66147J_1 EOG63FH1C_1 EOG61C70W_1 Dplexcds denovo54_f0 denovo184_f0 denovo314_f0 denovo392_f0 denovo496_f0 denovo548_f0 denovo626_f0 denovo652_f0 denovo678_f0 denovo704_f0 denovo756_f0 denovo808_f0 denovo834_f0 denovo860_f0 denovo886_f0 denovo912_f0 denovo990_f0 denovo1016_f0 denovo1094_f0 denovo1120_f0 denovo1172_f0 denovo1198_f0 denovo1250_f0 denovo1276_f0 denovo1328_f0 denovo1432_f0 denovo1458_f0 denovo1536_f0 denovo1562_f0 denovo1588_f0 denovo1614_f0 denovo1692_f0 denovo1718_f0 denovo1822_f0 denovo1848_f0 denovo1874_f0 denovo1900_f0 denovo2030_f0 denovo2056_f0 denovo2082_f0 denovo2160_f0 denovo2212_f0 denovo2316_f0 denovo2368_f0 denovo2394_f0 denovo2420_f0 denovo2550_f0 denovo2680_f0 denovo2706_f0 denovo2732_f0 denovo2810_f0 denovo2888_f0 denovo2940_f0 denovo2966_f0 denovo3018_f0 denovo3070_f0 denovo3096_f0 denovo3122_f0 denovo3174_f0 denovo3200_f0 denovo3356_f0 denovo3382_f0 denovo3408_f0 denovo3460_f0 denovo3512_f0 denovo3538_f0 denovo3564_f0 denovo3642_f0 denovo3876_f0 denovo3902_f0 denovo3928_f0 denovo4006_f0 denovo4084_f0 denovo4110_f0 denovo4136_f0 denovo4162_f0 denovo4214_f0 denovo4240_f0 denovo4266_f0 denovo4422_f0 denovo4474_f0 denovo4500_f0 denovo4526_f0 denovo4578_f0 denovo4604_f0 denovo4656_f0 denovo4682_f0 denovo4708_f0 denovo4812_f0 denovo4864_f0 denovo5020_f0 denovo5046_f0 denovo5072_f0 denovo5098_f0 denovo5124_f0 denovo5150_f0 denovo5176_f0 denovo5280_f0 denovo5306_f0 denovo5332_f0 denovo5358_f0 denovo5410_f0 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denovo207_f0 denovo337_f0 denovo415_f0 denovo519_f0 denovo571_f0 denovo649_f0 denovo675_f0 denovo701_f0 denovo727_f0 denovo779_f0 denovo831_f0 denovo857_f0 denovo883_f0 denovo909_f0 denovo935_f0 denovo1013_f0 denovo1039_f0 denovo1117_f0 denovo1143_f0 denovo1195_f0 denovo1221_f0 denovo1273_f0 denovo1299_f0 denovo1351_f0 denovo1455_f0 denovo1481_f0 denovo1559_f0 denovo1585_f0 denovo1611_f0 denovo1637_f0 denovo1715_f0 denovo1741_f0 denovo1845_f0 denovo1871_f0 denovo1897_f0 denovo1923_f0 denovo2053_f0 denovo2079_f0 denovo2105_f0 denovo2183_f0 denovo2235_f0 denovo2339_f0 denovo2391_f0 denovo2417_f0 denovo2443_f0 denovo2573_f0 denovo2703_f0 denovo2729_f0 denovo2755_f0 denovo2833_f0 denovo2911_f0 denovo2963_f0 denovo2989_f0 denovo3041_f0 denovo3093_f0 denovo3119_f0 denovo3145_f0 denovo3197_f0 denovo3223_f0 denovo3379_f0 denovo3405_f0 denovo3431_f0 denovo3483_f0 denovo3535_f0 denovo3561_f0 denovo3587_f0 denovo3665_f0 denovo3899_f0 denovo3925_f0 denovo3951_f0 denovo4029_f0 denovo4107_f0 denovo4133_f0 denovo4159_f0 denovo4185_f0 denovo4237_f0 denovo4263_f0 denovo4289_f0 denovo4445_f0 denovo4497_f0 denovo4523_f0 denovo4549_f0 denovo4601_f0 denovo4627_f0 denovo4679_f0 denovo4705_f0 denovo4731_f0 denovo4835_f0 denovo4887_f0 denovo5043_f0 denovo5069_f0 denovo5095_f0 denovo5121_f0 denovo5147_f0 denovo5173_f0 denovo5199_f0 denovo5303_f0 denovo5329_f0 denovo5355_f0 denovo5381_f0 denovo5433_f0 denovo5485_f0 denovo5511_f0 denovo5563_f0 denovo5589_f0 denovo5693_f0 denovo5719_f0 denovo5745_f0 denovo5771_f0 denovo5797_f0 denovo5823_f0 denovo5849_f0 denovo5875_f0 denovo5901_f0 denovo5927_f0 denovo6005_f0 denovo6057_f0 denovo6161_f0 denovo6187_f0 denovo6343_f0 denovo6369_f0 denovo6421_f0 denovo6447_f0 denovo6473_f0 denovo6499_f0 denovo6551_f0 denovo6655_f0 denovo6811_f0 denovo6863_f0 denovo6915_f0 denovo6941_f0 denovo6967_f0 denovo7045_f0 denovo7071_f0 denovo7123_f0 denovo7201_f0 denovo7227_f0 denovo7253_f0 denovo7461_f0 denovo7487_f0 denovo7617_f0 denovo7669_f0 denovo7747_f0 denovo7799_f0 denovo7877_f0 denovo7903_f0 denovo7955_f0 denovo7981_f0 denovo8033_f0 denovo8111_f0 denovo8137_f0 denovo8163_f0 denovo8189_f0 denovo8215_f0 denovo8345_f0 denovo8371_f0 denovo8501_f0 denovo8527_f0 denovo8553_f0 denovo8631_f0 denovo8735_f0 denovo8761_f0 denovo8813_f0 denovo8891_f0 denovo9047_f0 denovo9073_f0 denovo9099_f0 denovo9125_f0 denovo9229_f0 denovo9255_f0 denovo9281_f0 denovo9437_f0 denovo9489_f0 denovo9541_f0 denovo9593_f0 denovo9645_f0 denovo9671_f0 denovo9775_f0 denovo9931_f0 denovo10035_f0 denovo10061_f0 denovo10113_f0 denovo10139_f0 denovo10165_f0 denovo10269_f0 denovo10581_f0 denovo10607_f0 denovo10919_f0 denovo11075_f0 denovo11153_f0 denovo11231_f0 denovo11517_f0 denovo11543_f0 denovo11595_f0 denovo11621_f0 denovo11777_f0 denovo11881_f0 denovo11907_f0 denovo11959_f0 FG120071B denovo61_f0 denovo191_f0 denovo321_f0 denovo399_f0 denovo503_f0 denovo555_f0 denovo633_f0 denovo659_f0 denovo685_f0 denovo711_f0 denovo763_f0 denovo815_f0 denovo841_f0 denovo867_f0 denovo893_f0 denovo919_f0 denovo997_f0 denovo1023_f0 denovo1101_f0 denovo1127_f0 denovo1179_f0 denovo1205_f0 denovo1257_f0 denovo1283_f0 denovo1335_f0 denovo1439_f0 denovo1465_f0 denovo1543_f0 denovo1569_f0 denovo1595_f0 denovo1621_f0 denovo1699_f0 denovo1725_f0 denovo1829_f0 denovo1855_f0 denovo1881_f0 denovo1907_f0 denovo2037_f0 denovo2063_f0 denovo2089_f0 denovo2167_f0 denovo2219_f0 denovo2323_f0 denovo2375_f0 denovo2401_f0 denovo2427_f0 denovo2557_f0 denovo2687_f0 denovo2713_f0 denovo2739_f0 denovo2817_f0 denovo2895_f0 denovo2947_f0 denovo2973_f0 denovo3025_f0 denovo3077_f0 denovo3103_f0 denovo3129_f0 denovo3181_f0 denovo3207_f0 denovo3363_f0 denovo3389_f0 denovo3415_f0 denovo3467_f0 denovo3519_f0 denovo3545_f0 denovo3571_f0 denovo3649_f0 denovo3883_f0 denovo3909_f0 denovo3935_f0 denovo4013_f0 denovo4091_f0 denovo4117_f0 denovo4143_f0 denovo4169_f0 denovo4221_f0 denovo4247_f0 denovo4273_f0 denovo4429_f0 denovo4481_f0 denovo4507_f0 denovo4533_f0 denovo4585_f0 denovo4611_f0 denovo4663_f0 denovo4689_f0 denovo4715_f0 denovo4819_f0 denovo4871_f0 denovo5027_f0 denovo5053_f0 denovo5079_f0 denovo5105_f0 denovo5131_f0 denovo5157_f0 denovo5183_f0 denovo5287_f0 denovo5313_f0 denovo5339_f0 denovo5365_f0 denovo5417_f0 denovo5469_f0 denovo5495_f0 denovo5547_f0 denovo5573_f0 denovo5677_f0 denovo5703_f0 denovo5729_f0 denovo5755_f0 denovo5781_f0 denovo5807_f0 denovo5833_f0 denovo5859_f0 denovo5885_f0 denovo5911_f0 denovo5989_f0 denovo6041_f0 denovo6145_f0 denovo6171_f0 denovo6327_f0 denovo6353_f0 denovo6405_f0 denovo6431_f0 denovo6457_f0 denovo6483_f0 denovo6535_f0 denovo6639_f0 denovo6795_f0 denovo6847_f0 denovo6899_f0 denovo6925_f0 denovo6951_f0 denovo7029_f0 denovo7055_f0 denovo7107_f0 denovo7185_f0 denovo7211_f0 denovo7237_f0 denovo7445_f0 denovo7471_f0 denovo7601_f0 denovo7653_f0 denovo7731_f0 denovo7783_f0 denovo7861_f0 denovo7887_f0 denovo7939_f0 denovo7965_f0 denovo8017_f0 denovo8095_f0 denovo8121_f0 denovo8147_f0 denovo8173_f0 denovo8199_f0 denovo8329_f0 denovo8355_f0 denovo8485_f0 denovo8511_f0 denovo8537_f0 denovo8615_f0 denovo8719_f0 denovo8745_f0 denovo8797_f0 denovo8875_f0 denovo9031_f0 denovo9057_f0 denovo9083_f0 denovo9109_f0 denovo9213_f0 denovo9239_f0 denovo9265_f0 denovo9421_f0 denovo9473_f0 denovo9525_f0 denovo9577_f0 denovo9629_f0 denovo9655_f0 denovo9759_f0 denovo9915_f0 denovo10019_f0 denovo10045_f0 denovo10097_f0 denovo10123_f0 denovo10149_f0 denovo10253_f0 denovo10565_f0 denovo10591_f0 denovo10903_f0 denovo11059_f0 denovo11137_f0 denovo11215_f0 denovo11501_f0 denovo11527_f0 denovo11579_f0 denovo11605_f0 denovo11761_f0 denovo11865_f0 denovo11891_f0 denovo11943_f0 GNV120027 denovo65_f0 denovo195_f0 denovo325_f0 denovo403_f0 denovo507_f0 denovo559_f0 denovo637_f0 denovo663_f0 denovo689_f0 denovo715_f0 denovo767_f0 denovo819_f0 denovo845_f0 denovo871_f0 denovo897_f0 denovo923_f0 denovo1001_f0 denovo1027_f0 denovo1105_f0 denovo1131_f0 denovo1183_f0 denovo1209_f0 denovo1261_f0 denovo1287_f0 denovo1339_f0 denovo1443_f0 denovo1469_f0 denovo1547_f0 denovo1573_f0 denovo1599_f0 denovo1625_f0 denovo1703_f0 denovo1729_f0 denovo1833_f0 denovo1859_f0 denovo1885_f0 denovo1911_f0 denovo2041_f0 denovo2067_f0 denovo2093_f0 denovo2171_f0 denovo2223_f0 denovo2327_f0 denovo2379_f0 denovo2405_f0 denovo2431_f0 denovo2561_f0 denovo2691_f0 denovo2717_f0 denovo2743_f0 denovo2821_f0 denovo2899_f0 denovo2951_f0 denovo2977_f0 denovo3029_f0 denovo3081_f0 denovo3107_f0 denovo3133_f0 denovo3185_f0 denovo3211_f0 denovo3367_f0 denovo3393_f0 denovo3419_f0 denovo3471_f0 denovo3523_f0 denovo3549_f0 denovo3575_f0 denovo3653_f0 denovo3887_f0 denovo3913_f0 denovo3939_f0 denovo4017_f0 denovo4095_f0 denovo4121_f0 denovo4147_f0 denovo4173_f0 denovo4225_f0 denovo4251_f0 denovo4277_f0 denovo4433_f0 denovo4485_f0 denovo4511_f0 denovo4537_f0 denovo4589_f0 denovo4615_f0 denovo4667_f0 denovo4693_f0 denovo4719_f0 denovo4823_f0 denovo4875_f0 denovo5031_f0 denovo5057_f0 denovo5083_f0 denovo5109_f0 denovo5135_f0 denovo5161_f0 denovo5187_f0 denovo5291_f0 denovo5317_f0 denovo5343_f0 denovo5369_f0 denovo5421_f0 denovo5473_f0 denovo5499_f0 denovo5551_f0 denovo5577_f0 denovo5681_f0 denovo5707_f0 denovo5733_f0 denovo5759_f0 denovo5785_f0 denovo5811_f0 denovo5837_f0 denovo5863_f0 denovo5889_f0 denovo5915_f0 denovo5993_f0 denovo6045_f0 denovo6149_f0 denovo6175_f0 denovo6331_f0 denovo6357_f0 denovo6409_f0 denovo6435_f0 denovo6461_f0 denovo6487_f0 denovo6539_f0 denovo6643_f0 denovo6799_f0 denovo6851_f0 denovo6903_f0 denovo6929_f0 denovo6955_f0 denovo7033_f0 denovo7059_f0 denovo7111_f0 denovo7189_f0 denovo7215_f0 denovo7241_f0 denovo7449_f0 denovo7475_f0 denovo7605_f0 denovo7657_f0 denovo7735_f0 denovo7787_f0 denovo7865_f0 denovo7891_f0 denovo7943_f0 denovo7969_f0 denovo8021_f0 denovo8099_f0 denovo8125_f0 denovo8151_f0 denovo8177_f0 denovo8203_f0 denovo8333_f0 denovo8359_f0 denovo8489_f0 denovo8515_f0 denovo8541_f0 denovo8619_f0 denovo8723_f0 denovo8749_f0 denovo8801_f0 denovo8879_f0 denovo9035_f0 denovo9061_f0 denovo9087_f0 denovo9113_f0 denovo9217_f0 denovo9243_f0 denovo9269_f0 denovo9425_f0 denovo9477_f0 denovo9529_f0 denovo9581_f0 denovo9633_f0 denovo9659_f0 denovo9763_f0 denovo9919_f0 denovo10023_f0 denovo10049_f0 denovo10101_f0 denovo10127_f0 denovo10153_f0 denovo10257_f0 denovo10569_f0 denovo10595_f0 denovo10907_f0 denovo11063_f0 denovo11141_f0 denovo11219_f0 denovo11505_f0 denovo11531_f0 denovo11583_f0 denovo11609_f0 denovo11765_f0 denovo11869_f0 denovo11895_f0 denovo11947_f0 Bmoricds denovo52_f0 denovo182_f0 denovo312_f0 denovo390_f0 denovo494_f0 denovo546_f0 denovo624_f0 denovo650_f0 denovo676_f0 denovo702_f0 denovo754_f0 denovo806_f0 denovo832_f0 denovo858_f0 denovo884_f0 denovo910_f0 denovo988_f0 denovo1014_f0 denovo1092_f0 denovo1118_f0 denovo1170_f0 denovo1196_f0 denovo1248_f0 denovo1274_f0 denovo1326_f0 denovo1430_f0 denovo1456_f0 denovo1534_f0 denovo1560_f0 denovo1586_f0 denovo1612_f0 denovo1690_f0 denovo1716_f0 denovo1820_f0 denovo1846_f0 denovo1872_f0 denovo1898_f0 denovo2028_f0 denovo2054_f0 denovo2080_f0 denovo2158_f0 denovo2210_f0 denovo2314_f0 denovo2366_f0 denovo2392_f0 denovo2418_f0 denovo2548_f0 denovo2678_f0 denovo2704_f0 denovo2730_f0 denovo2808_f0 denovo2886_f0 denovo2938_f0 denovo2964_f0 denovo3016_f0 denovo3068_f0 denovo3094_f0 denovo3120_f0 denovo3172_f0 denovo3198_f0 denovo3354_f0 denovo3380_f0 denovo3406_f0 denovo3458_f0 denovo3510_f0 denovo3536_f0 denovo3562_f0 denovo3640_f0 denovo3874_f0 denovo3900_f0 denovo3926_f0 denovo4004_f0 denovo4082_f0 denovo4108_f0 denovo4134_f0 denovo4160_f0 denovo4212_f0 denovo4238_f0 denovo4264_f0 denovo4420_f0 denovo4472_f0 denovo4498_f0 denovo4524_f0 denovo4576_f0 denovo4602_f0 denovo4654_f0 denovo4680_f0 denovo4706_f0 denovo4810_f0 denovo4862_f0 denovo5018_f0 denovo5044_f0 denovo5070_f0 denovo5096_f0 denovo5122_f0 denovo5148_f0 denovo5174_f0 denovo5278_f0 denovo5304_f0 denovo5330_f0 denovo5356_f0 denovo5408_f0 denovo5460_f0 denovo5486_f0 denovo5538_f0 denovo5564_f0 denovo5668_f0 denovo5694_f0 denovo5720_f0 denovo5746_f0 denovo5772_f0 denovo5798_f0 denovo5824_f0 denovo5850_f0 denovo5876_f0 denovo5902_f0 denovo5980_f0 denovo6032_f0 denovo6136_f0 denovo6162_f0 denovo6318_f0 denovo6344_f0 denovo6396_f0 denovo6422_f0 denovo6448_f0 denovo6474_f0 denovo6526_f0 denovo6630_f0 denovo6786_f0 denovo6838_f0 denovo6890_f0 denovo6916_f0 denovo6942_f0 denovo7020_f0 denovo7046_f0 denovo7098_f0 denovo7176_f0 denovo7202_f0 denovo7228_f0 denovo7436_f0 denovo7462_f0 denovo7592_f0 denovo7644_f0 denovo7722_f0 denovo7774_f0 denovo7852_f0 denovo7878_f0 denovo7930_f0 denovo7956_f0 denovo8008_f0 denovo8086_f0 denovo8112_f0 denovo8138_f0 denovo8164_f0 denovo8190_f0 denovo8320_f0 denovo8346_f0 denovo8476_f0 denovo8502_f0 denovo8528_f0 denovo8606_f0 denovo8710_f0 denovo8736_f0 denovo8788_f0 denovo8866_f0 denovo9022_f0 denovo9048_f0 denovo9074_f0 denovo9100_f0 denovo9204_f0 denovo9230_f0 denovo9256_f0 denovo9412_f0 denovo9464_f0 denovo9516_f0 denovo9568_f0 denovo9620_f0 denovo9646_f0 denovo9750_f0 denovo9906_f0 denovo10010_f0 denovo10036_f0 denovo10088_f0 denovo10114_f0 denovo10140_f0 denovo10244_f0 denovo10556_f0 denovo10582_f0 denovo10894_f0 denovo11050_f0 denovo11128_f0 denovo11206_f0 denovo11492_f0 denovo11518_f0 denovo11570_f0 denovo11596_f0 denovo11752_f0 denovo11856_f0 denovo11882_f0 denovo11934_f0 Pcit2 denovo71_f0 denovo201_f0 denovo331_f0 denovo409_f0 denovo513_f0 denovo565_f0 denovo643_f0 denovo669_f0 denovo695_f0 denovo721_f0 denovo773_f0 denovo825_f0 denovo851_f0 denovo877_f0 denovo903_f0 denovo929_f0 denovo1007_f0 denovo1033_f0 denovo1111_f0 denovo1137_f0 denovo1189_f0 denovo1215_f0 denovo1267_f0 denovo1293_f0 denovo1345_f0 denovo1449_f0 denovo1475_f0 denovo1553_f0 denovo1579_f0 denovo1605_f0 denovo1631_f0 denovo1709_f0 denovo1735_f0 denovo1839_f0 denovo1865_f0 denovo1891_f0 denovo1917_f0 denovo2047_f0 denovo2073_f0 denovo2099_f0 denovo2177_f0 denovo2229_f0 denovo2333_f0 denovo2385_f0 denovo2411_f0 denovo2437_f0 denovo2567_f0 denovo2697_f0 denovo2723_f0 denovo2749_f0 denovo2827_f0 denovo2905_f0 denovo2957_f0 denovo2983_f0 denovo3035_f0 denovo3087_f0 denovo3113_f0 denovo3139_f0 denovo3191_f0 denovo3217_f0 denovo3373_f0 denovo3399_f0 denovo3425_f0 denovo3477_f0 denovo3529_f0 denovo3555_f0 denovo3581_f0 denovo3659_f0 denovo3893_f0 denovo3919_f0 denovo3945_f0 denovo4023_f0 denovo4101_f0 denovo4127_f0 denovo4153_f0 denovo4179_f0 denovo4231_f0 denovo4257_f0 denovo4283_f0 denovo4439_f0 denovo4491_f0 denovo4517_f0 denovo4543_f0 denovo4595_f0 denovo4621_f0 denovo4673_f0 denovo4699_f0 denovo4725_f0 denovo4829_f0 denovo4881_f0 denovo5037_f0 denovo5063_f0 denovo5089_f0 denovo5115_f0 denovo5141_f0 denovo5167_f0 denovo5193_f0 denovo5297_f0 denovo5323_f0 denovo5349_f0 denovo5375_f0 denovo5427_f0 denovo5479_f0 denovo5505_f0 denovo5557_f0 denovo5583_f0 denovo5687_f0 denovo5713_f0 denovo5739_f0 denovo5765_f0 denovo5791_f0 denovo5817_f0 denovo5843_f0 denovo5869_f0 denovo5895_f0 denovo5921_f0 denovo5999_f0 denovo6051_f0 denovo6155_f0 denovo6181_f0 denovo6337_f0 denovo6363_f0 denovo6415_f0 denovo6441_f0 denovo6467_f0 denovo6493_f0 denovo6545_f0 denovo6649_f0 denovo6805_f0 denovo6857_f0 denovo6909_f0 denovo6935_f0 denovo6961_f0 denovo7039_f0 denovo7065_f0 denovo7117_f0 denovo7195_f0 denovo7221_f0 denovo7247_f0 denovo7455_f0 denovo7481_f0 denovo7611_f0 denovo7663_f0 denovo7741_f0 denovo7793_f0 denovo7871_f0 denovo7897_f0 denovo7949_f0 denovo7975_f0 denovo8027_f0 denovo8105_f0 denovo8131_f0 denovo8157_f0 denovo8183_f0 denovo8209_f0 denovo8339_f0 denovo8365_f0 denovo8495_f0 denovo8521_f0 denovo8547_f0 denovo8625_f0 denovo8729_f0 denovo8755_f0 denovo8807_f0 denovo8885_f0 denovo9041_f0 denovo9067_f0 denovo9093_f0 denovo9119_f0 denovo9223_f0 denovo9249_f0 denovo9275_f0 denovo9431_f0 denovo9483_f0 denovo9535_f0 denovo9587_f0 denovo9639_f0 denovo9665_f0 denovo9769_f0 denovo9925_f0 denovo10029_f0 denovo10055_f0 denovo10107_f0 denovo10133_f0 denovo10159_f0 denovo10263_f0 denovo10575_f0 denovo10601_f0 denovo10913_f0 denovo11069_f0 denovo11147_f0 denovo11225_f0 denovo11511_f0 denovo11537_f0 denovo11589_f0 denovo11615_f0 denovo11771_f0 denovo11875_f0 denovo11901_f0 denovo11953_f0
2.8 Reconstruct the trees¶
This will build trees only for the supermatrices because we pass their names. First we configure the analysis using a RaxmlConf object and then we execute it.
The RaxmlConf object has several presets coresponding to several tree reconstruction approaches. These can be modified by using command line arguments. Alternatively, the program Phylobayes can be used with the PbConf object.
In [ ]:
raxml = RaxmlConf(pj,
method_name='fa',
program_name='raxmlHPC-PTHREADS-SSE3',
keepfiles=False, # RAxML result files are
# deleted by default
cmd='default',
preset='fa', # The default preset 'fa',
# will invoke the " -f a "
# algorithm. See manual for
# other presets
alns=aln_names, # Instead of the default value
# 'all', this object will apply
# only for the supermatrices
model='GAMMA', # Any RAxML model
matrix='JTT', # Any substitution matrix in RAxML.
# For DNA data, this defaults to GTR
cline_args={}, # Any RAxML keyword and argument.
# For example: {'#': 1000}, will change
# the default 100 rappid bootstrap
# replicates.
threads=6)
# reconstruct the trees
pj.tree([raxml])
raxmlHPC-PTHREADS-SSE3 -f a -m PROTGAMMAJTT -n 357421429738848.49_entropy_0.48_0.00_loci_50_to_2490 -q 357421429738848.49_entropy_0.48_0.00_loci_50_to_249_partfile -p 122 -s 357421429738848.49_entropy_0.48_0.00_loci_50_to_249.fasta -T 6 -x 388 -N 100 raxmlHPC-PTHREADS-SSE3 -f a -m PROTGAMMAJTT -n 357421429738848.49_entropy_0.00_0.00_loci_200_to_3990 -q 357421429738848.49_entropy_0.00_0.00_loci_200_to_399_partfile -p 607 -s 357421429738848.49_entropy_0.00_0.00_loci_200_to_399.fasta -T 6 -x 442 -N 100 raxmlHPC-PTHREADS-SSE3 -f a -m PROTGAMMAJTT -n 357421429738848.49_entropy_0.30_0.00_loci_100_to_2990 -q 357421429738848.49_entropy_0.30_0.00_loci_100_to_299_partfile -p 446 -s 357421429738848.49_entropy_0.30_0.00_loci_100_to_299.fasta -T 6 -x 186 -N 100 raxmlHPC-PTHREADS-SSE3 -f a -m PROTGAMMAJTT -n 357421429738848.49_entropy_1.14_0.00_loci_0_to_1990 -q 357421429738848.49_entropy_1.14_0.00_loci_0_to_199_partfile -p 748 -s 357421429738848.49_entropy_1.14_0.00_loci_0_to_199.fasta -T 6 -x 235 -N 100 raxmlHPC-PTHREADS-SSE3 -f a -m PROTGAMMAJTT -n 357421429738848.49_entropy_0.00_0.00_loci_150_to_3490 -q 357421429738848.49_entropy_0.00_0.00_loci_150_to_349_partfile -p 316 -s 357421429738848.49_entropy_0.00_0.00_loci_150_to_349.fasta -T 6 -x 679 -N 100
Note:¶
The value of -m is always PROT for concatenations. This is overridden by the partition file, where DNA will be specified for DNA partitions, envoking the GTR matrix of nucleic acid substitution. You can check the info file while the analysis runs or by using the keepfiles = True keyword to verify.
2.9 Verify git commit¶
At any step it is possible to confirm that git is working and recording the changes
In [24]:
print pj.last_git_log()
Sun Apr 26 08:44:54 2015 STDOUT: [master 6c085d7] RaxmlConf named fa with ID 357421429738848.49 Alignments: entropy_0.48_0.00_loci_50_to_249,entropy_0.00_0.00_loci_200_to_399,entropy_0.30_0.00_loci_100_to_299,entropy_1.14_0.00_loci_0_to_199,entropy_0.00_0.00_loci_150_to_349,entropy_0.00_0.00_loci_250_to_449 Created on: Wed Apr 22 22:40:48 2015 Commands: entropy_0.48_0.00_loci_50_to_249: [RaxmlCommandline(cmd='raxmlHPC-PTHREADS-SSE3', algorithm='a', model='PROTGAMMAJTT', name='357421429738848.49_entropy_0.48_0.00_loci_50_to_2490', partition_filename='357421429738848.49_entropy_0.48_0.00_loci_50_to_249_partfile', parsimony_seed=122, sequences='357421429738848.49_entropy_0.48_0.00_loci_50_to_249.fasta', threads=6, rapid_bootstrap_seed=388, num_replicates=100)] entropy_0.00_0.00_loci_200_to_399: [RaxmlCommandline(cmd='raxmlHPC-PTHREADS-SSE3', algorithm='a', model='PROTGAMMAJTT', name='357421429738848.49_entropy_0.00_0.00_loci_200_to_3990', partition_filename='357421429738848.49_entropy_0.00_0.00_loci_200_to_399_partfile', parsimony_seed=607, sequences='357421429738848.49_entropy_0.00_0.00_loci_200_to_399.fasta', threads=6, rapid_bootstrap_seed=442, num_replicates=100)] entropy_0.30_0.00_loci_100_to_299: [RaxmlCommandline(cmd='raxmlHPC-PTHREADS-SSE3', algorithm='a', model='PROTGAMMAJTT', name='357421429738848.49_entropy_0.30_0.00_loci_100_to_2990', partition_filename='357421429738848.49_entropy_0.30_0.00_loci_100_to_299_partfile', parsimony_seed=446, sequences='357421429738848.49_entropy_0.30_0.00_loci_100_to_299.fasta', threads=6, rapid_bootstrap_seed=186, num_replicates=100)] entropy_1.14_0.00_loci_0_to_199: [RaxmlCommandline(cmd='raxmlHPC-PTHREADS-SSE3', algorithm='a', model='PROTGAMMAJTT', name='357421429738848.49_entropy_1.14_0.00_loci_0_to_1990', partition_filename='357421429738848.49_entropy_1.14_0.00_loci_0_to_199_partfile', parsimony_seed=748, sequences='357421429738848.49_entropy_1.14_0.00_loci_0_to_199.fasta', threads=6, rapid_bootstrap_seed=235, num_replicates=100)] entropy_0.00_0.00_loci_150_to_349: [RaxmlCommandline(cmd='raxmlHPC-PTHREADS-SSE3', algorithm='a', model='PROTGAMMAJTT', name='357421429738848.49_entropy_0.00_0.00_loci_150_to_3490', partition_filename='357421429738848.49_entropy_0.00_0.00_loci_150_to_349_partfile', parsimony_seed=316, sequences='357421429738848.49_entropy_0.00_0.00_loci_150_to_349.fasta', threads=6, rapid_bootstrap_seed=679, num_replicates=100)] entropy_0.00_0.00_loci_250_to_449: [RaxmlCommandline(cmd='raxmlHPC-PTHREADS-SSE3', algorithm='a', model='PROTGAMMAJTT', name='357421429738848.49_entropy_0.00_0.00_loci_250_to_4490', partition_filename='357421429738848.49_entropy_0.00_0.00_loci_250_to_449_partfile', parsimony_seed=402, sequences='357421429738848.49_entropy_0.00_0.00_loci_250_to_449.fasta', threads=6, rapid_bootstrap_seed=649, num_replicates=100)] 5 files changed, 10155 insertions(+), 3689 deletions(-) create mode 100644 .ipynb_checkpoints/Untitled-checkpoint.ipynb create mode 100644 Untitled.ipynb STDERR:None >>>> None
2.10 Plot the trees - Figure 2A 1-6¶
In [28]:
# Remove stars from species names
from itertools import chain
for f in chain(*[r.features for r in pj.records]):
if 'Taxa' in f.qualifiers:
f.qualifiers['Taxa'][0] = f.qualifiers['Taxa'][0].replace('*','')
pj.propagate_metadata()
pics = {'Bombycoidea': 'silhouettes/Bombycoidea.png',
'Calliduloidea': 'silhouettes/Calliduloidea.png',
'Cossoidea': 'silhouettes/Cossoidea.png',
'Gelechioidea': 'silhouettes/Gelechioidea.png',
'Geometroidea': 'silhouettes/Geometroidea.png',
'Hepialoidea': 'silhouettes/Hepialoidea.png',
'Papilionoidea': 'silhouettes/Papilionoidea.png',
'Mimallonoidea': 'silhouettes/Mimallonoidea.png',
'Zygaenoidea': 'silhouettes/Zygaenoidea.png',
'Lasiocampoidea': 'silhouettes/Lasiocampoidea.png',
'Thyridoidea': 'silhouettes/Thyridoidea.png',
'Pterophoroidea': 'silhouettes/Pterophoroidea.png',
'Pyraloidea': 'silhouettes/Pyraloidea.png',
'Noctuoidea': 'silhouettes/Noctuoidea.png',
'Gracillarioidea': 'silhouettes/Gracillarioidea.png',
'Yponomeutoidea': 'silhouettes/Yponomeutoidea.png',
'Urodoidea': 'silhouettes/Urodoidea.png',
'Tortricoidea': 'silhouettes/Tortricoidea.png'
}
colors = {'Bombycoidea': 'DodgerBlue',
'Calliduloidea': 'DodgerBlue',
'Cossoidea': 'DodgerBlue',
'Gelechioidea': 'DodgerBlue',
'Geometroidea': 'DodgerBlue',
'Hepialoidea': 'DodgerBlue',
'Papilionoidea': 'SaddleBrown',
'Mimallonoidea': 'DodgerBlue',
'Zygaenoidea': 'DodgerBlue',
'Lasiocampoidea': 'DodgerBlue',
'Thyridoidea': 'DodgerBlue',
'Pterophoroidea': 'DodgerBlue',
'Pyraloidea': 'DodgerBlue',
'Noctuoidea': 'DodgerBlue',
'Gracillarioidea': 'DodgerBlue',
'Yponomeutoidea': 'DodgerBlue',
'Urodoidea': 'DodgerBlue',
'Tortricoidea': 'DodgerBlue'}
bg = {'butterfilies': 'LightSkyBlue',
'I': 'PowderBlue',
'III': 'LightGrey',
'IV': 'Beige'
}
supports = { 'DarkBlue' : [100,99],
'DimGray': [99,80]}
#'PaleTurquoise': [80,50]}
dir_name = "butterfly_figs"
html_name = "%s/figures.html"%dir_name
if not os.path.exists(dir_name):
os.mkdir(dir_name)
pj.clear_tree_annotations()
pj.annotate(dir_name, # Where to save the figures
'mid', # Root at midpoint. Alternatively, specify
'mid', # metadata and value to define outgroup
['Taxa'], # a list of metadata fields to use for labels
leaf_node_color_meta='source_Superfamily',
leaf_label_colors=colors,
ftype='Arial Black',
fsize=40,
node_support_dict=supports, # colors and ranges of node support annotations
support_bullet_size=15,
pic_meta='source_Superfamily',
pic_paths=pics,
pic_w=85, pic_h=65,
node_bg_meta='Clade',
node_bg_color=bg,
branch_width=6, branch_color='RoyalBlue',
scale=2500,
html=html_name)
In [1]:
from reprophylo import *
pj = unpickle_pj('szitenberg_et_al_15_reprophylo')
DEBUG:Cloud:Log file (/home/amir/.picloud/cloud.log) opened
/home/amir/Dropbox/python_modules/reprophylo.py:240: UserWarning: Git repository exists for this Project
warnings.warn('Git repository exists for this Project')
2.11 Robinson-foulds like metrics¶
In [2]:
# Sort the trees in sensible order (optional)
pj.trees.keys()
Out[2]:
['entropy_0.00_0.00_loci_250_to_449@mixed@mixed@fa', 'entropy_0.30_0.00_loci_100_to_299@mixed@mixed@fa', 'entropy_1.14_0.00_loci_0_to_199@mixed@mixed@fa', 'entropy_0.48_0.00_loci_50_to_249@mixed@mixed@fa', 'entropy_0.00_0.00_loci_200_to_399@mixed@mixed@fa', 'entropy_0.00_0.00_loci_150_to_349@mixed@mixed@fa']
In [2]:
trees = ['entropy_1.14_0.00_loci_0_to_199@mixed@mixed@fa',
'entropy_0.48_0.00_loci_50_to_249@mixed@mixed@fa',
'entropy_0.30_0.00_loci_100_to_299@mixed@mixed@fa',
'entropy_0.00_0.00_loci_150_to_349@mixed@mixed@fa',
'entropy_0.00_0.00_loci_200_to_399@mixed@mixed@fa',
'entropy_0.00_0.00_loci_250_to_449@mixed@mixed@fa',
]
2.11.1 Figure 2B: Topological¶
In [3]:
if not os.path.exists('rf_figs'):
os.mkdir('rf_figs')
# topological
figfile1, legend = calc_rf(pj, 'rf_figs', rf_type='topology', mp_root=True, trees=trees)
In [4]:
import IPython.display
IPython.display.Image(figfile1)
Out[4]:
In [5]:
print figfile1
rf_figs/1373.png
In [6]:
IPython.display.HTML(data=(HTML.table(legend[1:], header_row=legend[0])))
Out[6]:
| # | LOCUS | ALIGNMENT METHOD | TRIMMING METHOD | TREE METHOD |
|---|---|---|---|---|
| 1 | entropy_1.14_0.00_loci_0_to_199 | mixed | mixed | fa |
| 2 | entropy_0.48_0.00_loci_50_to_249 | mixed | mixed | fa |
| 3 | entropy_0.30_0.00_loci_100_to_299 | mixed | mixed | fa |
| 4 | entropy_0.00_0.00_loci_150_to_349 | mixed | mixed | fa |
| 5 | entropy_0.00_0.00_loci_200_to_399 | mixed | mixed | fa |
| 6 | entropy_0.00_0.00_loci_250_to_449 | mixed | mixed | fa |
Say we need to recall what Tree Metdod fa is:¶
In [13]:
print pj.used_methods['fa']
RaxmlConf named fa with ID 357421429738848.49 Alignments: entropy_0.48_0.00_loci_50_to_249,entropy_0.00_0.00_loci_200_to_399,entropy_0.30_0.00_loci_100_to_299,entropy_1.14_0.00_loci_0_to_199,entropy_0.00_0.00_loci_150_to_349,entropy_0.00_0.00_loci_250_to_449 Created on: Wed Apr 22 22:40:48 2015 Commands: entropy_0.48_0.00_loci_50_to_249: [RaxmlCommandline(cmd='raxmlHPC-PTHREADS-SSE3', algorithm='a', model='PROTGAMMAJTT', name='357421429738848.49_entropy_0.48_0.00_loci_50_to_2490', partition_filename='357421429738848.49_entropy_0.48_0.00_loci_50_to_249_partfile', parsimony_seed=122, sequences='357421429738848.49_entropy_0.48_0.00_loci_50_to_249.fasta', threads=6, rapid_bootstrap_seed=388, num_replicates=100)] entropy_0.00_0.00_loci_200_to_399: [RaxmlCommandline(cmd='raxmlHPC-PTHREADS-SSE3', algorithm='a', model='PROTGAMMAJTT', name='357421429738848.49_entropy_0.00_0.00_loci_200_to_3990', partition_filename='357421429738848.49_entropy_0.00_0.00_loci_200_to_399_partfile', parsimony_seed=607, sequences='357421429738848.49_entropy_0.00_0.00_loci_200_to_399.fasta', threads=6, rapid_bootstrap_seed=442, num_replicates=100)] entropy_0.30_0.00_loci_100_to_299: [RaxmlCommandline(cmd='raxmlHPC-PTHREADS-SSE3', algorithm='a', model='PROTGAMMAJTT', name='357421429738848.49_entropy_0.30_0.00_loci_100_to_2990', partition_filename='357421429738848.49_entropy_0.30_0.00_loci_100_to_299_partfile', parsimony_seed=446, sequences='357421429738848.49_entropy_0.30_0.00_loci_100_to_299.fasta', threads=6, rapid_bootstrap_seed=186, num_replicates=100)] entropy_1.14_0.00_loci_0_to_199: [RaxmlCommandline(cmd='raxmlHPC-PTHREADS-SSE3', algorithm='a', model='PROTGAMMAJTT', name='357421429738848.49_entropy_1.14_0.00_loci_0_to_1990', partition_filename='357421429738848.49_entropy_1.14_0.00_loci_0_to_199_partfile', parsimony_seed=748, sequences='357421429738848.49_entropy_1.14_0.00_loci_0_to_199.fasta', threads=6, rapid_bootstrap_seed=235, num_replicates=100)] entropy_0.00_0.00_loci_150_to_349: [RaxmlCommandline(cmd='raxmlHPC-PTHREADS-SSE3', algorithm='a', model='PROTGAMMAJTT', name='357421429738848.49_entropy_0.00_0.00_loci_150_to_3490', partition_filename='357421429738848.49_entropy_0.00_0.00_loci_150_to_349_partfile', parsimony_seed=316, sequences='357421429738848.49_entropy_0.00_0.00_loci_150_to_349.fasta', threads=6, rapid_bootstrap_seed=679, num_replicates=100)] entropy_0.00_0.00_loci_250_to_449: [RaxmlCommandline(cmd='raxmlHPC-PTHREADS-SSE3', algorithm='a', model='PROTGAMMAJTT', name='357421429738848.49_entropy_0.00_0.00_loci_250_to_4490', partition_filename='357421429738848.49_entropy_0.00_0.00_loci_250_to_449_partfile', parsimony_seed=402, sequences='357421429738848.49_entropy_0.00_0.00_loci_250_to_449.fasta', threads=6, rapid_bootstrap_seed=649, num_replicates=100)] Environment: Platform: Linux-3.13.0-40-generic-x86_64-with-Ubuntu-14.04-trusty Processor: x86_64 Python build: defaultMar 22 2014 22:59:56 Python compiler: GCC 4.8.2 Python implementation: CPython Python version: 2.7.6 ete2 version: 2.2rev1056 biopython version: 1.64 dendropy version: 3.12.0 cloud version: 2.8.5 reprophylo version 1.0 User: amir-TECRA-W50-A Program and version: raxmlHPC-PTHREADS-SSE3RAxML version 8.0.12 Program reference: A. Stamatakis: RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. In Bioinformatics 2014. execution time: 295421.237663 ============================== Core Methods section sentence: ============================== Phylogenetic trees were reconstructed from the dataset(s) entropy_0.48_0.00_loci_50_to_249;entropy_0.00_0.00_loci_200_to_399;entropy_0.30_0.00_loci_100_to_299;entropy_1.14_0.00_loci_0_to_199;entropy_0.00_0.00_loci_150_to_349;entropy_0.00_0.00_loci_250_to_449 using the program raxmlHPC-PTHREADS-SSE3RAxML version 8.0.12 [1]. Reference: A. Stamatakis: RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. In Bioinformatics, 2014.
2.11.2 Figure 2 C: Branch length¶
In [7]:
if not os.path.exists('rf_figs'):
os.mkdir('rf_figs')
# branch-length
figfile2, legend = calc_rf(pj, 'rf_figs', rf_type='branch-length', mp_root=True, trees=trees)
In [8]:
IPython.display.Image(figfile2)
Out[8]:
In [9]:
print figfile2
rf_figs/1615.png
In [10]:
IPython.display.HTML(data=(HTML.table(legend[1:], header_row=legend[0])))
Out[10]:
| # | LOCUS | ALIGNMENT METHOD | TRIMMING METHOD | TREE METHOD |
|---|---|---|---|---|
| 1 | entropy_1.14_0.00_loci_0_to_199 | mixed | mixed | fa |
| 2 | entropy_0.48_0.00_loci_50_to_249 | mixed | mixed | fa |
| 3 | entropy_0.30_0.00_loci_100_to_299 | mixed | mixed | fa |
| 4 | entropy_0.00_0.00_loci_150_to_349 | mixed | mixed | fa |
| 5 | entropy_0.00_0.00_loci_200_to_399 | mixed | mixed | fa |
| 6 | entropy_0.00_0.00_loci_250_to_449 | mixed | mixed | fa |
2.11.3 Figure 2 D: proportional¶
In [11]:
if not os.path.exists('rf_figs'):
os.mkdir('rf_figs')
import IPython.display
# topological
figfile3,legend = calc_rf(pj, 'rf_figs', rf_type='proportional', mp_root=True, trees=trees)
/home/amir/Dropbox/python_modules/reprophylo.py:5056: UserWarning: Trees must have the same taxa
warnings.warn('Trees must have the same taxa')
In [12]:
IPython.display.Image(figfile3)
Out[12]:
In [13]:
print figfile3
rf_figs/1024.png
In [14]:
IPython.display.HTML(data=(HTML.table(legend[1:], header_row=legend[0])))
Out[14]:
| # | LOCUS | ALIGNMENT METHOD | TRIMMING METHOD | TREE METHOD |
|---|---|---|---|---|
| 1 | entropy_1.14_0.00_loci_0_to_199 | mixed | mixed | fa |
| 2 | entropy_0.48_0.00_loci_50_to_249 | mixed | mixed | fa |
| 3 | entropy_0.30_0.00_loci_100_to_299 | mixed | mixed | fa |
| 4 | entropy_0.00_0.00_loci_150_to_349 | mixed | mixed | fa |
| 5 | entropy_0.00_0.00_loci_200_to_399 | mixed | mixed | fa |
| 6 | entropy_0.00_0.00_loci_250_to_449 | mixed | mixed | fa |
2.12 Prepare zip folder¶
In [3]:
publish(pj, 'report', 'butterfly_figs/',
compare_trees=['topology','branch-length','proportional'],
trees_to_compare=trees )
checking if file exists reporter was called by publish starting species table starting concatenations starting methods starting alignment statistics starting RF matrix(ces) reporting trees pickling archiving report ready
/home/amir/Dropbox/python_modules/reprophylo.py:5157: UserWarning: proportional branch-distance: Trees must have the same taxa
warnings.warn('proportional branch-distance: Trees must have the same taxa')
2.13 Add README¶
In [9]:
%%file README.md
This repository was automatically created and
maintained by [ReproPhylo V1](http://hulluni-bioinformatics.github.io/ReproPhylo/).
It contains the analysis done for the paper *ReproPhylo: a python package
for reproducible phylogenomics* by Amir Szitenberg, Max John, Mark Blaxter and David Lunt.
The data files in `data`, the ipython notebook and the pickled project `szitenberg_et_al_reprophylo`
were all versioned and commited automatically as the foundation of the experiments reproducibility.
The remaining files are manuscript related and where added manually later on.
All the figures in the repository were created by the workflow, as can be seen in the IPython Notebook,
or in its static copy, MethodsS1.html.
The commits list in this repository demonstrates the way in which ReproPhylo commits changes to the
repo and the automatically generated commit massages. Some are very informative, such as
[this one](https://github.com/HullUni-bioinformatics/Szitenberg_et_all_15-ReproPhylo/commit/6c085d736c9e9b9bfe8d3cc3b48e4c663ec8e190),
related to a commit of a tree reconstruction step.
Writing README.md
2.14 Manual commit of some additional files¶
In [7]:
# Just in case, commit the pickle again
pickle_pj(pj, "szitenberg_et_al_15_reprophylo")
Out[7]:
'szitenberg_et_al_15_reprophylo'
In [10]:
# files to add manually:
files=['rf_figs', 'butterfly_figs/', 'silhouettes/', 'MethodsS1.html, Figure1.pdf', 'Figure1.png',
'Figure2.pdf', 'Figure2.png', 'Figure2.png', 'plots.png', 'entropy.png',
'README.md']
for f in files:
rpgit.gitAdd(f)
rpgit.gitCommit('Additional files for the MS commited manually')
Out[10]:
('[master da6bc03] Additional files for the MS commited manually\n 1 file changed, 4 insertions(+)\n create mode 100644 README.md\n',
'')