Analysis Description -------------------- aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive random effects branch-site model framework to test whether each branch has evolved under positive selection, using a procedure which infers an optimal number of rate categories per branch. - __Requirements__: in-frame codon alignment and a phylogenetic tree - __Citation__: Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353 - __Written by__: Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group - __Contact Information__: spond@temple.edu - __Analysis Version__: 2.0 ####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-test/app/absrel/../../.hyphy/res//TemplateBatchFiles/SelectionAnalyses/`) >Loaded a multiple sequence alignment with **25** sequences, **424** codons, and **1** partitions from `/home/datamonkey/datamonkey-js-test/app/absrel/output/5b2fdfa218ed6e609e24690b` ####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 47 unlabeled branches >Please choose an option (or press q to cancel 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 47 unlabeled branches >Please choose an option (or press q to cancel 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 47 unlabeled branches >Please choose an option (or press q to cancel selection): ### * Selected 47 branches for testing: `BUSHBABY, MOUSE_LEMUR, COQUERELS_SIFAKA, Node3, TARSIER, BOLIVIAN_SQUIRREL_MONKEY, CAPUCHIN, Node10, MAS_NIGHT_MONKEY, MARMOSET, Node13, Node9, HUMAN, CHIMPANZEE, BONOBO, Node22, Node20, GORILLA, Node19, ORANGUTAN, Node18, GIBBON, Node17, SOOTY_MANGABEY, DRILL, Node32, OLIVE_BABOON, Node31, MACAQUE, CRAB_EATING_MACAQUE, Node37, PIG_TAILED_MACAQUE, Node36, Node30, VERVET, Node29, RED_COLOBUS, ANGOLA_COLOBUS, Node43, BLACK_SNUB_NOSED_MONKEY, GOLDEN_SNUB_NOSED_MONKEY, Node46, Node42, Node28, Node16, Node8, Node6` ### Obtaining branch lengths and nucleotide substitution biases under the nucleotide GTR model * Log(L) = -5660.68, AIC-c = 11431.55 (55 estimated parameters) ### Fitting the baseline model with a single dN/dS class per branch, and no site-to-site variation. * Log(L) = -5469.42, AIC-c = 11157.08 (108 estimated parameters) * Branch-level non-synonymous/synonymous rate ratio distribution has median 0.33, and 95% of the weight in 0.00 - 2.51 ### Determining the optimal number of rate classes per branch using a step up procedure | Branch | Length | Rates | Max. dN/dS | Log(L) | AIC-c |Best AIC-c so far| |-----------------------------------|----------|----------|--------------------|---------------|---------------|-----------------| | BUSHBABY | 0.10 | 2 | 0.48 (48.89%) | -5469.07 | 11160.47 | 11157.08 | | TARSIER | 0.09 | 2 | 1.42 (27.56%) | -5466.87 | 11156.07 | 11156.07 | | TARSIER | 0.09 | 3 | 1.58 (18.89%) | -5466.87 | 11160.16 | 11156.07 | | Node8 | 0.07 | 2 | 213.63 ( 0.97%) | -5464.15 | 11154.71 | 11154.71 | | Node8 | 0.07 | 3 | 213.52 ( 0.97%) | -5464.15 | 11158.80 | 11154.71 | | Node3 | 0.05 | 2 | 4.71 (11.97%) | -5460.39 | 11151.27 | 11151.27 | | Node3 | 0.05 | 3 | 5.59 ( 8.99%) | -5460.40 | 11155.39 | 11151.27 | | MOUSE_LEMUR | 0.05 | 2 | 2.32 (21.99%) | -5459.05 | 11152.69 | 11151.27 | | COQUERELS_SIFAKA | 0.04 | 2 | 0.32 (65.14%) | -5460.39 | 11155.36 | 11151.27 | | Node9 | 0.04 | 2 | 0.39 (99.86%) | -5460.38 | 11155.35 | 11151.27 | | Node6 | 0.03 | 2 | 63.09 ( 1.78%) | -5456.79 | 11148.18 | 11148.18 | | Node6 | 0.03 | 3 | 68.66 ( 1.72%) | -5456.79 | 11152.27 | 11148.18 | | MARMOSET | 0.03 | 2 | 0.33 (19.21%) | -5456.80 | 11152.27 | 11148.18 | | Node28 | 0.02 | 2 | 0.40 (97.71%) | -5456.79 | 11152.27 | 11148.18 | | BOLIVIAN_SQUIRREL_MONKEY | 0.02 | 2 | 0.25 (47.78%) | -5456.80 | 11152.28 | 11148.18 | | Node16 | 0.02 | 2 | 3.50 ( 5.30%) | -5456.61 | 11151.91 | 11148.18 | | ORANGUTAN | 0.02 | 2 | 0.32 (17.88%) | -5456.80 | 11152.28 | 11148.18 | | MAS_NIGHT_MONKEY | 0.01 | 2 | 0.42 (11.16%) | -5456.80 | 11152.27 | 11148.18 | | Node46 | 0.01 | 2 | 0.46 ( 2.64%) | -5456.79 | 11152.27 | 11148.18 | | GIBBON | 0.01 | 2 | >1000 ( 0.35%) | -5453.90 | 11146.48 | 11146.48 | | GIBBON | 0.01 | 3 | >1000 ( 0.34%) | -5453.90 | 11150.57 | 11146.48 | | CAPUCHIN | 0.01 | 2 | 0.50 (25.60%) | -5453.90 | 11150.57 | 11146.48 | | Node19 | 0.01 | 2 | 0.40 (49.70%) | -5453.90 | 11150.57 | 11146.48 | | VERVET | 0.01 | 2 | 0.40 (50.66%) | -5453.90 | 11150.57 | 11146.48 | | Node30 | 0.01 | 2 | 0.45 (30.11%) | -5453.90 | 11150.58 | 11146.48 | | RED_COLOBUS | 0.01 | 2 | 0.49 (29.20%) | -5453.91 | 11150.59 | 11146.48 | | OLIVE_BABOON | 0.01 | 2 | 0.25 (51.79%) | -5453.90 | 11150.58 | 11146.48 | | Node17 | 0.01 | 2 | 0.50 (50.67%) | -5453.90 | 11150.57 | 11146.48 | | HUMAN | 0.01 | 2 | >1000 ( 0.32%) | -5450.00 | 11142.77 | 11142.77 | | HUMAN | 0.01 | 3 | >1000 ( 0.32%) | -5450.00 | 11146.86 | 11142.77 | | ANGOLA_COLOBUS | 0.00 | 2 | 0.49 ( 5.59%) | -5450.00 | 11146.86 | 11142.77 | | Node10 | 0.00 | 2 | 0.00 (98.04%) | -5450.00 | 11146.86 | 11142.77 | | SOOTY_MANGABEY | 0.00 | 2 | 0.98 ( 4.88%) | -5450.00 | 11146.86 | 11142.77 | | Node29 | 0.00 | 2 | 0.67 (23.32%) | -5450.00 | 11146.87 | 11142.77 | | BONOBO | 0.00 | 2 | 0.74 ( 5.15%) | -5450.00 | 11146.86 | 11142.77 | | GORILLA | 0.00 | 2 | 0.50 (10.16%) | -5450.00 | 11146.86 | 11142.77 | | DRILL | 0.00 | 2 | 0.25 ( 0.00%) | -5450.00 | 11146.86 | 11142.77 | | Node43 | 0.00 | 2 | 0.25 ( 1.96%) | -5453.43 | 11153.72 | 11142.77 | | CRAB_EATING_MACAQUE | 0.00 | 2 | 0.25 ( 0.00%) | -5450.00 | 11146.86 | 11142.77 | | Node36 | 0.00 | 2 | 0.74 ( 4.91%) | -5450.00 | 11146.86 | 11142.77 | | PIG_TAILED_MACAQUE | 0.00 | 2 | 0.25 ( 0.00%) | -5450.00 | 11146.86 | 11142.77 | | Node22 | 0.00 | 2 | 0.00 (88.24%) | -5450.00 | 11146.86 | 11142.77 | | Node20 | 0.00 | 2 | 0.00 (98.04%) | -5450.00 | 11146.86 | 11142.77 | | BLACK_SNUB_NOSED_MONKEY | 0.00 | 2 | 736.30 (93.95%) | -5450.00 | 11146.87 | 11142.77 | | GOLDEN_SNUB_NOSED_MONKEY | 0.00 | 2 | 29.07 (100.00%) | -5450.01 | 11146.89 | 11142.77 | | CHIMPANZEE | 0.00 | 2 | 1.00 (100.00%) | -5450.35 | 11147.56 | 11142.77 | | MACAQUE | 0.00 | 2 | >1000 (38.49%) | -5450.00 | 11146.87 | 11142.77 | | Node18 | 0.00 | 2 | 0.25 ( 1.96%) | -5450.00 | 11146.86 | 11142.77 | | Node13 | 0.00 | 2 | 0.25 ( 1.96%) | -5450.00 | 11146.86 | 11142.77 | | Node31 | 0.00 | 2 | 0.25 ( 1.96%) | -5450.00 | 11146.86 | 11142.77 | | Node42 | 0.00 | 2 | 0.25 ( 1.96%) | -5450.00 | 11146.86 | 11142.77 | | Node32 | 0.00 | 2 | 0.25 ( 1.96%) | -5450.00 | 11146.86 | 11142.77 | | Node37 | 0.00 | 2 | 0.25 ( 1.96%) | -5450.00 | 11146.86 | 11142.77 | ### Rate class analyses summary * 41 branches with **1** rate classes * 6 branches with **2** rate classes ### Improving parameter estimates of the adaptive rate class model * Log(L) = -5442.30, AIC-c = 11127.38 (120 estimated parameters) ### Testing selected branches for selection | Branch | Rates | Max. dN/dS | Test LRT |Uncorrected p-value | |-----------------------------------|----------|--------------------|--------------------|--------------------| | BUSHBABY | 1 | 0.20 (100.00%) | 0.00 | 1.00000 | | TARSIER | 2 | 1.27 (28.39%) | 0.34 | 0.36614 | | Node8 | 2 | 230.57 ( 0.74%) | 1.85 | 0.15352 | | Node3 | 2 | 4.28 (11.68%) | 3.05 | 0.08160 | | MOUSE_LEMUR | 1 | 0.39 (100.00%) | 0.00 | 1.00000 | | COQUERELS_SIFAKA | 1 | 0.28 (100.00%) | 0.00 | 1.00000 | | Node9 | 1 | 0.36 (100.00%) | 0.00 | 1.00000 | | Node6 | 2 | 60.41 ( 1.78%) | 5.34 | 0.02490 | | MARMOSET | 1 | 0.23 (100.00%) | 0.00 | 1.00000 | | Node28 | 1 | 0.36 (100.00%) | 0.00 | 1.00000 | | BOLIVIAN_SQUIRREL_MONKEY | 1 | 0.14 (100.00%) | 0.00 | 1.00000 | | Node16 | 1 | 0.13 (100.00%) | 0.00 | 1.00000 | | ORANGUTAN | 1 | 0.09 (100.00%) | 0.00 | 1.00000 | | MAS_NIGHT_MONKEY | 1 | 0.22 (100.00%) | 0.00 | 1.00000 | | Node46 | 1 | 0.37 (100.00%) | 0.00 | 1.00000 | | GIBBON | 2 | >1000 ( 0.35%) | 5.48 | 0.02326 | | CAPUCHIN | 1 | 0.40 (100.00%) | 0.00 | 1.00000 | | Node19 | 1 | 0.29 (100.00%) | 0.00 | 1.00000 | | VERVET | 1 | 0.30 (100.00%) | 0.00 | 1.00000 | | Node30 | 1 | 0.27 (100.00%) | 0.00 | 1.00000 | | RED_COLOBUS | 1 | 0.16 (100.00%) | 0.00 | 1.00000 | | OLIVE_BABOON | 1 | 0.13 (100.00%) | 0.00 | 1.00000 | | Node17 | 1 | 0.43 (100.00%) | 0.00 | 1.00000 | | HUMAN | 2 | >1000 ( 0.32%) | 8.44 | 0.00513 | | ANGOLA_COLOBUS | 1 | 0.37 (100.00%) | 0.00 | 1.00000 | | Node10 | 1 | 0.00 (100.00%) | 0.00 | 1.00000 | | SOOTY_MANGABEY | 1 | 0.57 (100.00%) | 0.00 | 1.00000 | | Node29 | 1 | 0.15 (100.00%) | 0.00 | 1.00000 | | BONOBO | 1 | 0.38 (100.00%) | 0.00 | 1.00000 | | GORILLA | 1 | 0.37 (100.00%) | 0.00 | 1.00000 | | DRILL | 1 | 0.00 (100.00%) | 0.00 | 1.00000 | | Node43 | 1 | >1000 (100.00%) | 0.80 | 0.27488 | | CRAB_EATING_MACAQUE | 1 | 0.00 (100.00%) | 0.00 | 1.00000 | | Node36 | 1 | 0.38 (100.00%) | 0.00 | 1.00000 | | PIG_TAILED_MACAQUE | 1 | 0.00 (100.00%) | 0.00 | 1.00000 | | Node22 | 1 | 0.00 (100.00%) | 0.00 | 1.00000 | | Node20 | 1 | 0.00 (100.00%) | 0.00 | 1.00000 | | BLACK_SNUB_NOSED_MONKEY | 1 | >1000 (100.00%) | 0.63 | 0.30425 | | GOLDEN_SNUB_NOSED_MONKEY | 1 | >1000 (100.00%) | 0.64 | 0.30192 |