Analysis Description -------------------- FEL (Fixed Effects Likelihood) estimates site-wise synonymous (α) and non-synonymous (β) rates, and uses a likelihood ratio test to determine if beta &neq; alpha at a site. The estimates aggregate information over all branches, so the signal is derived from pervasive diversification or conservation. A subset of branches can be selected for testing as well, in which case an additional (nuisance) parameter will be inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported for recombination - aware analysis. - __Requirements__: in-frame codon alignment and a phylogenetic tree - __Citation__: Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222 - __Written by__: Sergei L Kosakovsky Pond and Simon DW Frost - __Contact Information__: spond@temple.edu - __Analysis Version__: 2.00 ####Choose Genetic Code 1. [**Universal**] Universal code. (Genebank transl_table=1). 2. [**Vertebrate mtDNA**] Vertebrate mitochondrial DNA code. (Genebank transl_table=2). 3. [**Yeast mtDNA**] Yeast mitochondrial DNA code. (Genebank transl_table=3). 4. [**Mold/Protozoan mtDNA**] Mold, Protozoan and Coelenterate mitochondrial DNA and the Mycloplasma/Spiroplasma code. (Genebank transl_table=4). 5. [**Invertebrate mtDNA**] Invertebrate mitochondrial DNA code. (Genebank transl_table=5). 6. [**Ciliate Nuclear**] Ciliate, Dasycladacean and Hexamita Nuclear code. (Genebank transl_table=6). 7. [**Echinoderm mtDNA**] Echinoderm mitochondrial DNA code. (Genebank transl_table=9). 8. [**Euplotid Nuclear**] Euplotid Nuclear code. (Genebank transl_table=10). 9. [**Alt. Yeast Nuclear**] Alternative Yeast Nuclear code. (Genebank transl_table=12). 10. [**Ascidian mtDNA**] Ascidian mitochondrial DNA code. (Genebank transl_table=13). 11. [**Flatworm mtDNA**] Flatworm mitochondrial DNA code. (Genebank transl_table=14). 12. [**Blepharisma Nuclear**] Blepharisma Nuclear code. (Genebank transl_table=15). 13. [**Chlorophycean mtDNA**] Chlorophycean Mitochondrial Code (transl_table=16). 14. [**Trematode mtDNA**] Trematode Mitochondrial Code (transl_table=21). 15. [**Scenedesmus obliquus mtDNA**] Scenedesmus obliquus mitochondrial Code (transl_table=22). 16. [**Thraustochytrium mtDNA**] Thraustochytrium Mitochondrial Code (transl_table=23). 17. [**Pterobranchia mtDNA**] Pterobranchia Mitochondrial Code (transl_table=24). 18. [**SR1 and Gracilibacteria**] Candidate Division SR1 and Gracilibacteria Code (transl_table=25). 19. [**Pachysolen Nuclear**] Pachysolen tannophilus Nuclear Code (transl_table=26). >Please choose an option (or press q to cancel selection): >Select a coding sequence alignment file (`/home/datamonkey/datamonkey-js-server/production/app/fel/../../.hyphy/res//TemplateBatchFiles/SelectionAnalyses/`) >Please select a tree file for the data: (`/home/datamonkey/datamonkey-js-server/production/app/fel/../../.hyphy/res//TemplateBatchFiles/SelectionAnalyses/`) >Loaded a multiple sequence alignment with **3** sequences, **346** codons, and **1** partitions from `/home/datamonkey/datamonkey-js-server/production/app/fel/output/5bfedc673feafb13311f9a7c` ####Choose the set of branches to test for selection 1. [**All**] Include all branches in the analysis 2. [**Internal**] Include all internal branches in the analysis 3. [**Leaves**] Include all leaf branches in the analysis 4. [**Unlabeled branches**] Set of 1 unlabeled branches 5. [**FG**] Set FG with 2 branches >Please choose an option (or press q to cancel selection): ####Use synonymous rate variation? Strongly recommended YES for selection inference. 1. [**Yes**] [Recommended] Consider synonymous rate variation (dS varies across sites). 2. [**No**] Ignore synonymous rate variation (dS := 1 at each site). >Please choose an option (or press q to cancel selection):Yes >Select the p-value threshold to use when testing for selection (permissible range = [0,1], default value = 0.1): ### Branches to include in the FEL analysis Selected 2 branches to include in FEL calculations: `S_LITTORALIS, S_EXIGUA` ### Obtaining branch lengths and nucleotide substitution biases under the nucleotide GTR model * Log(L) = -2064.02, AIC-c = 4150.13 (11 estimated parameters) ### Obtaining the global omega estimate based on relative GTR branch lengths and nucleotide substitution biases * Log(L) = -2091.20, AIC-c = 4221.14 (19 estimated parameters) * non-synonymous/synonymous rate ratio for *background* = 10000.0000 * non-synonymous/synonymous rate ratio for *test* = 0.1335 ### Improving branch lengths, nucleotide substitution biases, and global dN/dS ratios under a full codon model * Log(L) = -2091.20 * non-synonymous/synonymous rate ratio for *background* = 10000.0000 * non-synonymous/synonymous rate ratio for *test* = 0.1335 ### For partition 1 these sites are significant at p <=0.1 | Codon | Partition | alpha | beta | LRT |Selection detected?| |:--------------:|:--------------:|:--------------:|:--------------:|:--------------:|:-----------------:| | 3 | 1 | 11.039 | 0.000 | 3.645 | Neg. p = 0.0562 | | 4 | 1 | 13.270 | 0.000 | 4.726 | Neg. p = 0.0297 | | 5 | 1 | 11.038 | 0.000 | 3.887 | Neg. p = 0.0487 | | 9 | 1 | 23.410 | 0.000 | 5.215 | Neg. p = 0.0224 | | 10 | 1 | 9.997 | 0.000 | 4.742 | Neg. p = 0.0294 | | 37 | 1 | 11.039 | 0.000 | 4.614 | Neg. p = 0.0317 | | 38 | 1 | 10000.000 | 0.000 | 6.016 | Neg. p = 0.0142 | | 47 | 1 | 11.038 | 0.000 | 4.410 | Neg. p = 0.0357 | | 59 | 1 | 8708.486 | 0.000 | 7.318 | Neg. p = 0.0068 | | 70 | 1 | 224.484 | 0.000 | 6.009 | Neg. p = 0.0142 | | 92 | 1 | 11.038 | 0.000 | 4.669 | Neg. p = 0.0307 | | 198 | 1 | 11.038 | 0.000 | 4.669 | Neg. p = 0.0307 | | 104 | 1 | 22.796 | 0.000 | 5.471 | Neg. p = 0.0193 | | 106 | 1 | 29.961 | 0.000 | 7.136 | Neg. p = 0.0076 | | 133 | 1 | 22.797 | 0.000 | 6.112 | Neg. p = 0.0134 | | 168 | 1 | 9.118 | 0.000 | 3.005 | Neg. p = 0.0830 | | 172 | 1 | 47.504 | 0.000 | 2.940 | Neg. p = 0.0864 | | 205 | 1 | 667.591 | 0.000 | 4.886 | Neg. p = 0.0271 | | 215 | 1 | 11.039 | 0.000 | 3.888 | Neg. p = 0.0486 | | 252 | 1 | 11.038 | 0.000 | 4.474 | Neg. p = 0.0344 | | 253 | 1 | 3894.983 | 0.000 | 6.052 | Neg. p = 0.0139 | | 270 | 1 | 7293.741 | 0.000 | 8.408 | Neg. p = 0.0037 | | 306 | 1 | 1132.944 | 0.000 | 7.106 | Neg. p = 0.0077 | | 309 | 1 | 10000.000 | 0.000 | 9.523 | Neg. p = 0.0020 | | 324 | 1 | 178.085 | 0.000 | 4.418 | Neg. p = 0.0356 | | 339 | 1 | 10.203 | 0.000 | 3.926 | Neg. p = 0.0475 |