P A U P * Version 4.0b10 for 32-bit Microsoft Windows Fri May 09 20:03:07 2008 -----------------------------NOTICE----------------------------- This is a beta-test version. Please report any crashes, apparent calculation errors, or other anomalous results. There are no restrictions on publication of results obtained with this version, but you should check the WWW site frequently for bug announcements and/or updated versions. See the README file on the distribution media for details. ---------------------------------------------------------------- Character-status summary: Current optimality criterion = parsimony No characters are excluded Of 1506 total characters: All characters are of type 'unord' All characters have equal weight 271 characters are constant 188 variable characters are parsimony-uninformative Number of parsimony-informative characters = 1047 Taxon-status summary: Original data matrix contains 12 taxa No taxa have been deleted No taxa have been assigned to the outgroup: outgroup defaults to first taxon (E histolytica) Evaluating 200 trees sampled equiprobably from the set of all possible trees Trees are unrooted Starting seed = 1766568820 Optimality criterion = parsimony Character-status summary: Of 1506 total characters: All characters are of type 'unord' All characters have equal weight 271 characters are constant 188 variable characters are parsimony-uninformative Number of parsimony-informative characters = 1047 Gaps are treated as "missing" Time used = 0.06 sec Frequency distribution of lengths of 200 random trees: mean=4779.365000 sd=174.241102 g1=-0.717912 g2=0.149703 4194.00000 /------------------------------------------------------------- 4238.70000 +##### (2) 4283.40000 + (0) 4328.10000 + (0) 4372.80000 +##### (2) 4417.50000 +##### (2) 4462.20000 +############ (5) 4506.90000 +################# (7) 4551.60000 +#################### (8) 4596.30000 +########## (4) 4641.00000 +########################### (11) 4685.70000 +################################## (14) 4730.40000 +################################## (14) 4775.10000 +######################################### (17) 4819.80000 +############################################## (19) 4864.50000 +############################################################# (25) 4909.20000 +################################################# (20) 4953.90000 +##################################### (15) 4998.60000 +###################################################### (22) 5043.30000 +########################### (11) 5088.00000 +##### (2) \------------------------------------------------------------- Character-exclusion status changed: 459 characters excluded Total number of characters now excluded = 459 Number of included characters = 1047 Heuristic search settings: Optimality criterion = parsimony Character-status summary: 459 characters are excluded Of the remaining 1047 included characters: All characters are of type 'unord' All characters have equal weight All characters are parsimony-informative Gaps are treated as "missing" Starting tree(s) obtained via stepwise addition Addition sequence: as-is Number of trees held at each step during stepwise addition = 1 Branch-swapping algorithm: tree-bisection-reconnection (TBR) Steepest descent option not in effect Initial 'MaxTrees' setting = 100 (will be auto-increased by 100) Branches collapsed (creating polytomies) if maximum branch length is zero 'MulTrees' option in effect Topological constraints not enforced Trees are unrooted Heuristic search completed Total number of rearrangements tried = 540 Score of best tree(s) found = 3330 Number of trees retained = 1 Time used = 0.05 sec Tree number 1 (rooted using default outgroup) /--------------------------------------------------------------- E histolytica | | /----------- T brucei | /---------+ | | \----------- L major +-----------------------------------------+ | \--------------------- G lamblia | | /----------- T annulata | /-----------------------------------------+ | | \----------- T parva | | | | /------------------------------------------ P falciparum \---------+ | | | /----------- P berghei | | /---------+ \----------+ | \----------- P yoelii | /----------+ | | \--------------------- P chabaudi \---------+ | /----------- P knowlesi \--------------------+ \----------- P vivax 1 tree saved to file "D:\PHD\PAML analysis\GK v2\protozoa\PAUP DAMBE data\mp.tre" Lengths and fit measures of trees in memory: Character-status summary: 459 characters are excluded Of the remaining 1047 included characters: All characters are of type 'unord' All characters have equal weight All characters are parsimony-informative Gaps are treated as "missing" Sum of min. possible lengths = 2113 Sum of max. possible lengths = 5055 Tree # 1 Length 3330 CI 0.635 RI 0.586 HI 0.365 Bootstrap method with heuristic search: Number of bootstrap replicates = 500 Starting seed = 2054174454 Optimality criterion = parsimony Character-status summary: 459 characters are excluded Of the remaining 1047 included characters: All characters are of type 'unord' All characters have equal weight All characters are parsimony-informative Gaps are treated as "missing" Starting tree(s) obtained via stepwise addition Addition sequence: as-is Number of trees held at each step during stepwise addition = 1 Branch-swapping algorithm: tree-bisection-reconnection (TBR) Steepest descent option not in effect Initial 'MaxTrees' setting = 100 (will be auto-increased by 100) Branches collapsed (creating polytomies) if maximum branch length is zero 'MulTrees' option in effect Topological constraints not enforced Trees are unrooted 500 bootstrap replicates completed Time used = 11.64 sec Bootstrap 50% majority-rule consensus tree /----------------------------------------------------------- E histolytica(1) | | /---------- T brucei(2) | /---100---+ | | \---------- L major(3) +-----------------100------------------+ | \-------------------- G lamblia(12) | | /---------- T annulata(4) | /-----------------100------------------+ | | \---------- T parva(5) | | | | /--------------------------------------- P falciparum(6) \---59----+ | | | /---------- P berghei(7) | | /---100---+ \---100---+ | \---------- P yoelii(8) | /---100---+ | | \-------------------- P chabaudi(11) \---85---+ | /---------- P knowlesi(9) \--------100--------+ \---------- P vivax(10) Bipartitions found in one or more trees and frequency of occurrence (bootstrap support values): 1 1 123456789012 Freq % ----------------------------- ........**.. 500.00 100.0% ...**....... 500.00 100.0% ......**..*. 500.00 100.0% .**......... 500.00 100.0% .....******. 500.00 100.0% .**........* 499.00 99.8% ......**.... 497.67 99.5% ......*****. 424.83 85.0% ...********. 293.33 58.7% .****......* 149.67 29.9% .....***..*. 61.17 12.2% .**..******* 57.00 11.4% 3 groups at (relative) frequency less than 5% not shown 1 tree saved to file "D:\PHD\PAML analysis\GK v2\protozoa\PAUP DAMBE data\mpboot.tre" Optimality criterion set to distance. Warning: Distance matrix contains 7 undefined distance(s). These have been arbitrarily set to 2 times the maximum defined distance (=> 6.343759). HKY85 distance matrix 459 characters are excluded 1 2 3 4 5 6 1 E histolytica - 2 T brucei *6.34376 - 3 L major *6.34376 0.75630 - 4 T annulata 1.75503 3.17188 1.00000 - 5 T parva 1.63522 2.49076 1.00000 0.25146 - 6 P falciparum 1.24055 1.00000 *6.34376 2.01440 1.79126 - 7 P berghei 1.43571 1.00000 1.00000 1.78727 1.93595 0.42266 8 P yoelii 1.37376 0.42376 0.45661 1.73004 1.77887 0.41331 9 P knowlesi 1.72162 1.00000 *6.34376 1.73186 1.70711 0.54478 10 P vivax 2.06261 2.33399 2.23432 2.02331 2.01759 0.58403 11 P chabaudi 1.44988 *6.34376 0.39341 1.61998 1.62258 0.39970 12 G lamblia 2.28181 1.67714 1.80837 2.23634 2.76784 2.14364 HKY85 distance matrix (continued) 7 8 9 10 11 12 7 P berghei - 8 P yoelii 0.05029 - 9 P knowlesi 0.52263 0.52610 - 10 P vivax 0.63205 0.64594 0.20862 - 11 P chabaudi 0.10178 0.09712 0.47686 0.60155 - 12 G lamblia 2.79935 *6.34376 2.20659 2.10032 *6.34376 - * Undefined distance Neighbor-joining search settings: Ties (if encountered) will be broken systematically Distance measure = HKY85 459 characters are excluded (Tree is unrooted) Tree found by neighbor-joining method stored in tree buffer Time used = 0.00 sec Neighbor-joining tree: /--------------------- E histolytica | | /------- T brucei | /----+ | | \--------- L major | /-------------------+ | | \------------------------ G lamblia +------------------+ | | /-- T annulata | \-----+ | \-- T parva | | /---- P falciparum | | | | /- P berghei | | | \--+/---+/ P yoelii || \+ || \-- P chabaudi \+ | /- P knowlesi \-----+ \--- P vivax Processing TREES block from file "mpboot.tre": Keeping: trees from file (replacing trees in memory) 1 tree read from file Time used = 0.03 sec 1 tree now in memory Likelihood scores of tree(s) in memory: 459 characters are excluded Likelihood settings: Number of substitution types = 2 (HKY85 variant) Transition/transversion ratio estimated via ML Assumed nucleotide frequencies (empirical frequencies): A=0.34690 C=0.18250 G=0.20660 T=0.26400 Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to the HKY85+G model Number of distinct data patterns under this model = 992 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Tree 1 ------------------------- -ln L 11961.96857 Ti/tv: exp. ratio 1.430004 kappa 2.948782 Shape 2.277727 Time used to compute likelihoods = 20.78 sec Optimality criterion set to likelihood. Heuristic search settings: Optimality criterion = likelihood 459 characters are excluded Likelihood settings: Number of substitution types = 2 (HKY85 variant) Transition/transversion ratio = 1.43 (kappa = 2.9487819) Assumed nucleotide frequencies (empirical frequencies): A=0.34690 C=0.18250 G=0.20660 T=0.26400 Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = 2.27773 Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to the HKY85+G model Number of distinct data patterns under this model = 992 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Starting tree(s) obtained via stepwise addition Addition sequence: as-is Number of trees held at each step during stepwise addition = 1 Branch-swapping algorithm: tree-bisection-reconnection (TBR) Steepest descent option not in effect Initial 'MaxTrees' setting = 100 (will be auto-increased by 100) Branches collapsed (creating polytomies) if branch length is less than or equal to 1e-008 'MulTrees' option in effect Topological constraints not enforced Trees are unrooted Heuristic search completed Total number of rearrangements tried = 534 Score of best tree(s) found = 11961.97337 Number of trees retained = 1 Time used = 00:02:11.5 Tree number 1 (rooted using default outgroup) /--------------------------------------------------------------- E histolytica | | /----------- T brucei | /---------+ | | \----------- L major +-----------------------------------------+ | \--------------------- G lamblia | | /----------- T annulata | /-----------------------------------------+ | | \----------- T parva | | | | /------------------------------------------ P falciparum \---------+ | | | /----------- P berghei | | /---------+ \----------+ | \----------- P yoelii | /----------+ | | \--------------------- P chabaudi \---------+ | /----------- P knowlesi \--------------------+ \----------- P vivax 1 tree saved to file "D:\PHD\PAML analysis\GK v2\protozoa\PAUP DAMBE data\ml.tre" Bootstrap method with heuristic search: Number of bootstrap replicates = 500 Starting seed = 204049331 Optimality criterion = likelihood 459 characters are excluded Likelihood settings: Number of substitution types = 2 (HKY85 variant) Transition/transversion ratio = 1.43 (kappa = 2.9487819) Assumed nucleotide frequencies (empirical frequencies): A=0.34690 C=0.18250 G=0.20660 T=0.26400 Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = 2.27773 Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to the HKY85+G model Number of distinct data patterns under this model = 992 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Starting tree(s) obtained via stepwise addition Addition sequence: as-is Number of trees held at each step during stepwise addition = 1 Branch-swapping algorithm: tree-bisection-reconnection (TBR) Steepest descent option not in effect Initial 'MaxTrees' setting = 100 (will be auto-increased by 100) Branches collapsed (creating polytomies) if branch length is less than or equal to 1e-008 'MulTrees' option in effect Topological constraints not enforced Trees are unrooted Note: Approximation limit dynamically readjusted to 10.197831 Note: Approximation limit dynamically readjusted to 10.153019 Note: Approximation limit dynamically readjusted to 10.484501 Note: Approximation limit dynamically readjusted to 10.113893 Note: Approximation limit dynamically readjusted to 10.634196 Note: Approximation limit dynamically readjusted to 10.471990 Note: Approximation limit dynamically readjusted to 10.182011 Note: Approximation limit dynamically readjusted to 10.293098 Note: Approximation limit dynamically readjusted to 10.652603 Note: Approximation limit dynamically readjusted to 10.026945 500 bootstrap replicates completed Time used = 17:02:19.7 Bootstrap 50% majority-rule consensus tree /----------------------------------------------------------- E histolytica(1) | | /--------------- T brucei(2) | /------93------+ | | \--------------- L major(3) +-------------92-------------+ | \------------------------------ G lamblia(12) | | /--------------- T annulata(4) | /------------100-------------+ | | \--------------- T parva(5) | | | +-------------------------------------------- P falciparum(6) | | | | /--------------- P berghei(7) \------91------+ /------90------+ | | \--------------- P yoelii(8) +-----84------+ | \------------------------------ P chabaudi(11) | | /--------------- P knowlesi(9) \-------------54-------------+ \--------------- P vivax(10) Bipartitions found in one or more trees and frequency of occurrence (bootstrap support values): 1 1 123456789012 Freq % ----------------------------- ...**....... 500.00 100.0% .**......... 465.00 93.0% .**........* 459.00 91.8% ...********. 454.00 90.8% ......**.... 450.50 90.1% ......**..*. 420.50 84.1% ........**.. 272.00 54.4% .....******. 237.00 47.4% ...**.*****. 193.00 38.6% ......*****. 181.00 36.2% ...**...*... 170.00 34.0% ...**...**.. 158.00 31.6% ...**.**..*. 48.00 9.6% .....***..*. 46.00 9.2% .....*..**.. 43.00 8.6% .**********. 39.00 7.8% ...**.....*. 39.00 7.8% ...******.*. 34.00 6.8% .*.........* 29.00 5.8% 44 groups at (relative) frequency less than 5% not shown 1 tree saved to file "D:\PHD\PAML analysis\GK v2\protozoa\PAUP DAMBE data\mlboot.tre"