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 **27** sequences, **617** codons, and **1** partitions from `/home/datamonkey/datamonkey-js-server/production/app/fel/output/5c23a269bdd1573ada2103c7` ####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. [**FG**] Set FG with 51 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 51 branches to include in FEL calculations: `MVS_SFAX_TUN_09_09_4, MVS_MANCHESTER_GBR_7_12_2_B3_, MVI_NEW_JERSEY_USA_45_05_, Node10, MVI_LYON_FRA_20_04_, Node9, Node7, MVI_IBADAN_NGA_0_97_, MVI_MURCIA_ESP_18_03_, MVI_IBADAN_NGA_10_98_6, Node17, MVI_KHARTOUM_SDN_28_00_6, MVI_CAEN_FRA_0_04_, MVS_GERA_DEU_08_00_, MVI_SEGUERE_BFA_19_01_, Node26, MVI_LYON_FRA_0_94_, Node25, MVI_NEW_YORK_USA_0_94_, MVI_ACCRA_GHA_9_98_3, Node30, Node24, Node22, Node20, Node16, Node14, Node6, MVI_YAOUNDE_CMR_9_01_, Node5, MVI_CALAIS_FRA_01_16_B3_, Node4, MVS_CAPETOWN_ZAF_52_14, Node3, MVS_NEWCASTLEUPONTYNE_GBR_9_14_B3_, MVI_KAOHSIUNG_TWN_07_14_B3_, Node37, MVS_LONDON_GBR_41_13_B3_, MVS_DARTFORD_GBR_2_14_B3_, Node42, MVI_TAICHUNG_TWN_16_14, Node41, MVS_LONDON_GBR_4_14_2_B3_, Node40, Node36, Node2, MVS_CAPETOWN_ZAF_16_10_2_B3_, Node1, MVS_BRITISHCOLUMBIA_CAN_34_13_B3_, MVI_BERLIN_DEU_11_10, Node48, MVS_QUEBEC_CAN_26_13_` ### Obtaining branch lengths and nucleotide substitution biases under the nucleotide GTR model * Log(L) = -3891.99, AIC-c = 7902.12 (59 estimated parameters) ### Obtaining the global omega estimate based on relative GTR branch lengths and nucleotide substitution biases * Log(L) = -3791.30, AIC-c = 7715.13 (66 estimated parameters) * non-synonymous/synonymous rate ratio for *test* = 0.2301 ### Improving branch lengths, nucleotide substitution biases, and global dN/dS ratios under a full codon model * Log(L) = -3791.30 * non-synonymous/synonymous rate ratio for *test* = 0.2301 ### For partition 1 these sites are significant at p <=0.1 | Codon | Partition | alpha | beta | LRT |Selection detected?| |:--------------:|:--------------:|:--------------:|:--------------:|:--------------:|:-----------------:| | 6 | 1 | 7.797 | 0.000 | 3.142 | Neg. p = 0.0763 | | 11 | 1 | 7.774 | 0.000 | 2.814 | Neg. p = 0.0934 | | 14 | 1 | 6.355 | 0.000 | 2.838 | Neg. p = 0.0920 | | 43 | 1 | 7.788 | 0.000 | 2.815 | Neg. p = 0.0934 | | 80 | 1 | 9.192 | 0.000 | 4.261 | Neg. p = 0.0390 | | 83 | 1 | 8.780 | 0.000 | 3.717 | Neg. p = 0.0539 | | 97 | 1 | 11.613 | 0.000 | 5.344 | Neg. p = 0.0208 | | 119 | 1 | 9.872 | 0.000 | 4.305 | Neg. p = 0.0380 | | 139 | 1 | 7.415 | 0.000 | 3.001 | Neg. p = 0.0832 | | 141 | 1 | 7.774 | 0.000 | 3.203 | Neg. p = 0.0735 | | 237 | 1 | 9.929 | 0.000 | 4.552 | Neg. p = 0.0329 | | 238 | 1 | 6.416 | 0.000 | 2.908 | Neg. p = 0.0881 | | 241 | 1 | 7.544 | 0.000 | 3.401 | Neg. p = 0.0652 | | 361 | 1 | 6.406 | 0.000 | 2.910 | Neg. p = 0.0880 | | 420 | 1 | 8.457 | 0.000 | 4.500 | Neg. p = 0.0339 | | 426 | 1 | 6.092 | 0.000 | 2.786 | Neg. p = 0.0951 | | 431 | 1 | 7.797 | 0.000 | 2.815 | Neg. p = 0.0934 | | 435 | 1 | 6.447 | 0.000 | 2.738 | Neg. p = 0.0980 | | 450 | 1 | 6.379 | 0.000 | 2.902 | Neg. p = 0.0885 | | 461 | 1 | 6.355 | 0.000 | 2.898 | Neg. p = 0.0887 | | 494 | 1 | 7.544 | 0.000 | 3.021 | Neg. p = 0.0822 | | 505 | 1 | 7.544 | 0.000 | 3.090 | Neg. p = 0.0788 | | 513 | 1 | 7.415 | 0.000 | 3.129 | Neg. p = 0.0769 | | 541 | 1 | 8.150 | 0.000 | 2.766 | Neg. p = 0.0963 |