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 **22** sequences, **250** codons, and **1** partitions from `/home/datamonkey/datamonkey-js-test/app/absrel/output/5b2fde2918ed6e609e246830` ####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 41 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 41 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 41 unlabeled branches >Please choose an option (or press q to cancel selection): ### * Selected 41 branches for testing: `BUSHBABY, MOUSE_LEMUR, COQUERELS_SIFAKA, Node3, BOLIVIAN_SQUIRREL_MONKEY, CAPUCHIN, Node8, MAS_NIGHT_MONKEY, MARMOSET, Node11, Node7, HUMAN, BONOBO, Node18, GORILLA, Node17, ORANGUTAN, Node16, GIBBON, Node15, DRILL, OLIVE_BABOON, Node27, MACAQUE, CRAB_EATING_MACAQUE, Node31, PIG_TAILED_MACAQUE, Node30, Node26, VERVET, Node25, RED_COLOBUS, ANGOLA_COLOBUS, Node37, BLACK_SNUB_NOSED_MONKEY, GOLDEN_SNUB_NOSED_MONKEY, Node40, Node36, Node24, Node14, Node6` ### Obtaining branch lengths and nucleotide substitution biases under the nucleotide GTR model * Log(L) = -2793.09, AIC-c = 5684.48 (49 estimated parameters) ### Fitting the baseline model with a single dN/dS class per branch, and no site-to-site variation. * Log(L) = -2671.22, AIC-c = 5537.89 (96 estimated parameters) * Branch-level non-synonymous/synonymous rate ratio distribution has median 0.34, and 95% of the weight in 0.00 - 10000000000.00 ### 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 | 0.58 (26.01%) | -2671.19 | 5541.97 | 5537.89 | | Node6 | 0.07 | 2 | 6.23 (11.76%) | -2663.84 | 5527.28 | 5527.28 | | Node6 | 0.07 | 3 | 6.24 (11.76%) | -2663.84 | 5531.42 | 5527.28 | | MOUSE_LEMUR | 0.06 | 2 | 0.94 (26.35%) | -2663.28 | 5530.30 | 5527.28 | | Node3 | 0.06 | 2 | 2.90 ( 8.45%) | -2661.47 | 5526.67 | 5526.67 | | Node3 | 0.06 | 3 | 2.91 ( 8.43%) | -2661.47 | 5530.83 | 5526.67 | | BOLIVIAN_SQUIRREL_MONKEY | 0.02 | 2 | 0.39 (51.32%) | -2661.47 | 5530.83 | 5526.67 | | CAPUCHIN | 0.02 | 2 | 0.38 (51.77%) | -2661.47 | 5530.83 | 5526.67 | | Node14 | 0.02 | 2 | 12.36 ( 2.91%) | -2658.63 | 5525.15 | 5525.15 | | Node14 | 0.02 | 3 | 12.41 ( 2.90%) | -2658.63 | 5529.30 | 5525.15 | | Node7 | 0.02 | 2 | 0.74 (74.31%) | -2658.58 | 5529.21 | 5525.15 | | MAS_NIGHT_MONKEY | 0.02 | 2 | 0.91 (21.25%) | -2658.63 | 5529.30 | 5525.15 | | MARMOSET | 0.02 | 2 | 0.77 (84.58%) | -2658.63 | 5529.30 | 5525.15 | | ORANGUTAN | 0.02 | 2 | 0.24 ( 1.70%) | -2658.63 | 5529.30 | 5525.15 | | COQUERELS_SIFAKA | 0.01 | 2 | 0.40 (88.65%) | -2658.58 | 5529.20 | 5525.15 | | GIBBON | 0.01 | 2 | 0.25 (50.80%) | -2658.63 | 5529.30 | 5525.15 | | RED_COLOBUS | 0.01 | 2 | 0.22 (23.63%) | -2658.63 | 5529.31 | 5525.15 | | VERVET | 0.01 | 2 | 0.76 (50.63%) | -2658.63 | 5529.30 | 5525.15 | | Node17 | 0.01 | 2 | 0.20 (93.79%) | -2658.63 | 5529.30 | 5525.15 | | Node24 | 0.01 | 2 | 27.23 ( 1.79%) | -2658.60 | 5529.25 | 5525.15 | | Node40 | 0.01 | 2 | 0.60 (74.73%) | -2658.63 | 5529.30 | 5525.15 | | ANGOLA_COLOBUS | 0.01 | 2 | 1.99 (50.66%) | -2658.63 | 5529.31 | 5525.15 | | Node15 | 0.01 | 2 | 0.49 (24.19%) | -2658.63 | 5529.30 | 5525.15 | | Node11 | 0.00 | 2 | 0.00 (98.93%) | -2658.63 | 5529.30 | 5525.15 | | Node36 | 0.00 | 2 | 0.25 ( 0.00%) | -2658.63 | 5529.30 | 5525.15 | | Node37 | 0.00 | 2 | 0.75 (25.09%) | -2658.63 | 5529.30 | 5525.15 | | PIG_TAILED_MACAQUE | 0.00 | 2 | 0.50 (48.35%) | -2658.63 | 5529.30 | 5525.15 | | HUMAN | 0.00 | 2 | 0.75 (25.09%) | -2658.63 | 5529.30 | 5525.15 | | GORILLA | 0.00 | 2 | 311.72 (63.60%) | -2658.63 | 5529.32 | 5525.15 | | Node8 | 0.00 | 2 | 0.00 (98.04%) | -2658.63 | 5529.30 | 5525.15 | | Node16 | 0.00 | 2 | 0.25 ( 0.00%) | -2658.63 | 5529.30 | 5525.15 | | Node18 | 0.00 | 2 | 0.25 ( 0.00%) | -2658.63 | 5529.30 | 5525.15 | | Node26 | 0.00 | 2 | 0.25 ( 0.00%) | -2658.63 | 5529.30 | 5525.15 | | Node27 | 0.00 | 2 | 0.25 ( 0.00%) | -2658.63 | 5529.30 | 5525.15 | | CRAB_EATING_MACAQUE | 0.00 | 2 | 368.61 (100.00%) | -2658.63 | 5529.31 | 5525.15 | | GOLDEN_SNUB_NOSED_MONKEY | 0.00 | 2 | 1.00 (100.00%) | -2658.93 | 5529.90 | 5525.15 | | Node30 | 0.00 | 2 | 258.48 (39.49%) | -2658.63 | 5529.31 | 5525.15 | | DRILL | 0.00 | 2 | 180.15 (78.57%) | -2658.63 | 5529.31 | 5525.15 | | Node25 | 0.00 | 2 | 1.00 (100.00%) | -2658.77 | 5529.58 | 5525.15 | | BONOBO | 0.00 | 2 | 0.25 ( 1.96%) | -2658.63 | 5529.30 | 5525.15 | | BLACK_SNUB_NOSED_MONKEY | 0.00 | 2 | 0.25 ( 1.96%) | -2658.63 | 5529.30 | 5525.15 | | MACAQUE | 0.00 | 2 | 0.25 ( 1.96%) | -2658.63 | 5529.30 | 5525.15 | | OLIVE_BABOON | 0.00 | 2 | 0.25 ( 1.96%) | -2658.63 | 5529.30 | 5525.15 | | Node31 | 0.00 | 2 | 0.25 ( 1.96%) | -2658.63 | 5529.30 | 5525.15 | ### Rate class analyses summary * 38 branches with **1** rate classes * 3 branches with **2** rate classes ### Improving parameter estimates of the adaptive rate class model * Log(L) = -2656.50, AIC-c = 5520.90 (102 estimated parameters) ### Testing selected branches for selection | Branch | Rates | Max. dN/dS | Test LRT |Uncorrected p-value | |-----------------------------------|----------|--------------------|--------------------|--------------------| | BUSHBABY | 1 | 0.30 (100.00%) | 0.00 | 1.00000 | | Node6 | 2 | 6.00 (11.72%) | 6.96 | 0.01089 | | MOUSE_LEMUR | 1 | 0.23 (100.00%) | 0.00 | 1.00000 | | Node3 | 2 | 2.69 ( 8.49%) | 0.99 | 0.24752 | | BOLIVIAN_SQUIRREL_MONKEY | 1 | 0.32 (100.00%) | 0.00 | 1.00000 | | CAPUCHIN | 1 | 0.30 (100.00%) | 0.00 | 1.00000 | | Node14 | 2 | 12.23 ( 2.88%) | 3.04 | 0.08198 | | Node7 | 1 | 0.67 (100.00%) | 0.00 | 1.00000 | | MAS_NIGHT_MONKEY | 1 | 0.83 (100.00%) | 0.00 | 1.00000 | | MARMOSET | 1 | 0.69 (100.00%) | 0.00 | 1.00000 | | ORANGUTAN | 1 | 0.19 (100.00%) | 0.00 | 1.00000 | | COQUERELS_SIFAKA | 1 | 0.37 (100.00%) | 0.00 | 1.00000 | | GIBBON | 1 | 0.22 (100.00%) | 0.00 | 1.00000 | | RED_COLOBUS | 1 | 0.05 (100.00%) | 0.00 | 1.00000 | | VERVET | 1 | 0.65 (100.00%) | 0.00 | 1.00000 | | Node17 | 1 | 0.18 (100.00%) | 0.00 | 1.00000 | | Node24 | 1 | 0.50 (100.00%) | 0.00 | 1.00000 | | Node40 | 1 | 0.49 (100.00%) | 0.00 | 1.00000 | | ANGOLA_COLOBUS | 1 | 1.37 (100.00%) | 0.08 | 0.44467 | | Node15 | 1 | 0.24 (100.00%) | 0.00 | 1.00000 | | Node11 | 1 | 0.00 (100.00%) | 0.00 | 1.00000 | | Node36 | 1 | 0.00 (100.00%) | 0.00 | 1.00000 | | Node37 | 1 | 0.32 (100.00%) | 0.00 | 1.00000 | | PIG_TAILED_MACAQUE | 1 | 0.33 (100.00%) | 0.00 | 1.00000 | | HUMAN | 1 | 0.32 (100.00%) | 0.00 | 1.00000 | | GORILLA | 1 | >1000 (100.00%) | 1.02 | 0.24227 | | Node8 | 1 | 0.00 (100.00%) | 0.00 | 1.00000 | | Node16 | 1 | 0.00 (100.00%) | 0.00 | 1.00000 | | Node18 | 1 | 0.00 (100.00%) | 0.00 | 1.00000 | | Node26 | 1 | 0.00 (100.00%) | 0.00 | 1.00000 | | Node27 | 1 | 0.00 (100.00%) | 0.00 | 1.00000 | | CRAB_EATING_MACAQUE | 1 | >1000 (100.00%) | 0.57 | 0.31584 |