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, **243** codons, and **1** partitions from `/home/datamonkey/datamonkey-js-test/app/absrel/output/5b2fdde918ed6e609e246814` ####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: `PIKA, RABBIT, SQUIRREL, MARMOT, Node5, DEGU, LONG_TAILED_CHINCHILLA, Node11, GUINEA_PIG, Node10, NAKED_MOLE_RAT, DAMARA_MOLE_RAT, Node15, Node9, BEAVER, KANGAROO_RAT, Node19, LESSER_EGYPTIAN_JERBOA, BLIND_MOLE_RAT, HOUSE_MOUSE, RYUKYU_MOUSE, Node30, SHREW_MOUSE, Node29, RAT, Node28, MONGOLIAN_GERBIL, Node27, CHINESE_HAMSTER, GOLDEN_HAMSTER, Node38, PRAIRIE_VOLE, Node37, DEER_MOUSE, Node36, Node26, Node24, Node22, Node18, Node8, Node4` ### Obtaining branch lengths and nucleotide substitution biases under the nucleotide GTR model * Log(L) = -7012.98, AIC-c = 14124.27 (49 estimated parameters) ### Fitting the baseline model with a single dN/dS class per branch, and no site-to-site variation. * Log(L) = -6761.21, AIC-c = 13717.98 (96 estimated parameters) * Branch-level non-synonymous/synonymous rate ratio distribution has median 0.36, and 95% of the weight in 0.10 - 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| |-----------------------------------|----------|----------|--------------------|---------------|---------------|-----------------| | LESSER_EGYPTIAN_JERBOA | 0.18 | 2 | 6.50 ( 7.88%) | -6751.88 | 13703.46 | 13703.46 | | LESSER_EGYPTIAN_JERBOA | 0.18 | 3 | 160.60 ( 3.80%) | -6751.53 | 13706.91 | 13703.46 | | KANGAROO_RAT | 0.14 | 2 | 0.72 (27.46%) | -6751.61 | 13707.08 | 13703.46 | | BEAVER | 0.11 | 2 | 2.27 (22.62%) | -6746.98 | 13697.82 | 13697.82 | | BEAVER | 0.11 | 3 | 2.31 (22.39%) | -6746.98 | 13701.98 | 13697.82 | | PIKA | 0.10 | 2 | 0.10 (54.72%) | -6746.98 | 13701.97 | 13697.82 | | DEGU | 0.10 | 2 | 1.28 (33.08%) | -6744.99 | 13697.99 | 13697.82 | | BLIND_MOLE_RAT | 0.10 | 2 | 24.90 ( 2.16%) | -6744.51 | 13697.02 | 13697.02 | | BLIND_MOLE_RAT | 0.10 | 3 | 23.88 ( 2.24%) | -6744.50 | 13701.18 | 13697.02 | | Node5 | 0.10 | 2 | 0.88 (25.51%) | -6744.28 | 13700.73 | 13697.02 | | Node4 | 0.09 | 2 | 3.25 (17.01%) | -6736.56 | 13685.28 | 13685.28 | | Node4 | 0.09 | 3 | 3.92 (12.34%) | -6736.57 | 13689.47 | 13685.28 | | GOLDEN_HAMSTER | 0.09 | 2 | 0.34 (59.78%) | -6736.56 | 13689.45 | 13685.28 | | MONGOLIAN_GERBIL | 0.08 | 2 | 0.63 (48.82%) | -6736.48 | 13689.30 | 13685.28 | | Node9 | 0.07 | 2 | >1000 ( 2.24%) | -6731.70 | 13679.73 | 13679.73 | | Node9 | 0.07 | 3 | >1000 ( 2.23%) | -6731.70 | 13683.90 | 13679.73 | | GUINEA_PIG | 0.07 | 2 | 0.57 (44.25%) | -6731.44 | 13683.38 | 13679.73 | | RAT | 0.07 | 2 | 1.67 (27.83%) | -6731.11 | 13682.72 | 13679.73 | | PRAIRIE_VOLE | 0.06 | 2 | 9.02 ( 4.52%) | -6727.37 | 13675.23 | 13675.23 | | PRAIRIE_VOLE | 0.06 | 3 | 287.83 ( 0.93%) | -6726.01 | 13676.69 | 13675.23 | | DEER_MOUSE | 0.06 | 2 | 0.38 (83.25%) | -6727.37 | 13679.40 | 13675.23 | | Node29 | 0.06 | 2 | 0.58 (39.11%) | -6727.37 | 13679.40 | 13675.23 | | NAKED_MOLE_RAT | 0.05 | 2 | 1.95 (16.78%) | -6725.95 | 13676.56 | 13675.23 | | DAMARA_MOLE_RAT | 0.05 | 2 | 0.16 (100.00%) | -6727.36 | 13679.39 | 13675.23 | | Node24 | 0.05 | 2 | 15.18 ( 2.44%) | -6725.66 | 13675.99 | 13675.23 | | Node26 | 0.05 | 2 | 8.63 ( 5.20%) | -6725.54 | 13675.74 | 13675.23 | | RABBIT | 0.04 | 2 | 0.16 (100.00%) | -6727.36 | 13679.38 | 13675.23 | | CHINESE_HAMSTER | 0.04 | 2 | 7.85 ( 9.28%) | -6723.07 | 13670.80 | 13670.80 | | CHINESE_HAMSTER | 0.04 | 3 | 8.95 ( 7.77%) | -6723.07 | 13674.99 | 13670.80 | | SHREW_MOUSE | 0.04 | 2 | 25.55 ( 2.06%) | -6721.53 | 13671.90 | 13670.80 | | LONG_TAILED_CHINCHILLA | 0.04 | 2 | 0.75 (49.84%) | -6723.04 | 13674.92 | 13670.80 | | Node38 | 0.04 | 2 | 4.39 ( 9.26%) | -6721.68 | 13672.20 | 13670.80 | | Node22 | 0.03 | 2 | 7.71 ( 4.30%) | -6720.18 | 13669.20 | 13669.20 | | Node22 | 0.03 | 3 | 7.81 ( 4.29%) | -6720.18 | 13673.37 | 13669.20 | | Node36 | 0.02 | 2 | 4.35 ( 9.23%) | -6719.02 | 13671.04 | 13669.20 | | Node28 | 0.02 | 2 | 749.35 (59.39%) | -6720.22 | 13673.44 | 13669.20 | | Node10 | 0.02 | 2 | 28.54 ( 6.94%) | -6717.07 | 13667.16 | 13667.16 | | Node10 | 0.02 | 3 | 30.73 ( 6.87%) | -6717.08 | 13671.34 | 13667.16 | | RYUKYU_MOUSE | 0.02 | 2 | 1.69 (56.73%) | -6717.08 | 13671.35 | 13667.16 | | Node30 | 0.02 | 2 | 0.18 (100.00%) | -6717.07 | 13671.34 | 13667.16 | | Node11 | 0.01 | 2 | 30.34 ( 1.75%) | -6715.86 | 13668.90 | 13667.16 | | SQUIRREL | 0.01 | 2 | 0.49 (26.15%) | -6717.08 | 13671.34 | 13667.16 | | Node8 | 0.01 | 2 | 0.58 (96.38%) | -6716.90 | 13670.99 | 13667.16 | | HOUSE_MOUSE | 0.01 | 2 | 1.03 (10.69%) | -6717.07 | 13671.34 | 13667.16 | | Node15 | 0.01 | 2 | 8.98 ( 9.99%) | -6717.03 | 13671.25 | 13667.16 | | Node19 | 0.01 | 2 | 3.23 (100.00%) | -6717.06 | 13671.30 | 13667.16 | | MARMOT | 0.01 | 2 | 0.50 (51.39%) | -6717.07 | 13671.34 | 13667.16 | | Node27 | 0.01 | 2 | 0.49 (26.64%) | -6717.07 | 13671.33 | 13667.16 | | Node18 | 0.01 | 2 | >1000 ( 1.92%) | -6716.47 | 13670.13 | 13667.16 | | Node37 | 0.00 | 2 | 0.25 ( 1.96%) | -6719.20 | 13675.59 | 13667.16 | ### Rate class analyses summary * 9 branches with **2** rate classes * 32 branches with **1** rate classes ### Improving parameter estimates of the adaptive rate class model * Log(L) = -6707.64, AIC-c = 13648.29 (114 estimated parameters) ### Testing selected branches for selection | Branch | Rates | Max. dN/dS | Test LRT |Uncorrected p-value | |-----------------------------------|----------|--------------------|--------------------|--------------------| | LESSER_EGYPTIAN_JERBOA | 2 | 6.35 ( 7.75%) | 3.08 | 0.08016 | | KANGAROO_RAT | 1 | 0.28 (100.00%) | 0.00 | 1.00000 | | BEAVER | 2 | 2.16 (22.50%) | 1.95 | 0.14567 | | PIKA | 1 | 0.09 (100.00%) | 0.00 | 1.00000 | | DEGU | 1 | 0.33 (100.00%) | 0.00 | 1.00000 | | BLIND_MOLE_RAT | 2 | 22.24 ( 2.61%) | 2.15 | 0.13087 | | Node5 | 1 | 0.30 (100.00%) | 0.00 | 1.00000 | | Node4 | 2 | 3.15 (16.87%) | 4.65 | 0.03560 | | GOLDEN_HAMSTER | 1 | 0.29 (100.00%) | 0.00 | 1.00000 | | MONGOLIAN_GERBIL | 1 | 0.35 (100.00%) | 0.00 | 1.00000 | | Node9 | 2 | >1000 ( 2.42%) | 4.65 | 0.03551 | | GUINEA_PIG | 1 | 0.22 (100.00%) | 0.00 | 1.00000 | | RAT | 1 | 0.40 (100.00%) | 0.00 | 1.00000 | | PRAIRIE_VOLE | 2 | 4.89 (10.99%) | 4.19 | 0.04505 | | DEER_MOUSE | 1 | 0.34 (100.00%) | 0.00 | 1.00000 | | Node29 | 1 | 0.52 (100.00%) | 0.00 | 1.00000 | | NAKED_MOLE_RAT | 1 | 0.25 (100.00%) | 0.00 | 1.00000 | | DAMARA_MOLE_RAT | 1 | 0.16 (100.00%) | 0.00 | 1.00000 | | Node24 | 1 | 0.29 (100.00%) | 0.00 | 1.00000 | | Node26 | 1 | 0.25 (100.00%) | 0.00 | 1.00000 | | RABBIT | 1 | 0.15 (100.00%) | 0.00 | 1.00000 | | CHINESE_HAMSTER | 2 | 7.61 ( 9.16%) | 5.47 | 0.02339 | | SHREW_MOUSE | 1 | 0.70 (100.00%) | 0.00 | 1.00000 | | LONG_TAILED_CHINCHILLA | 1 | 0.36 (100.00%) | 0.00 | 1.00000 | | Node38 | 1 | 0.36 (100.00%) | 0.00 | 1.00000 | | Node22 | 2 | 6.73 ( 4.55%) | 2.59 | 0.10391 | | Node36 | 1 | 0.34 (100.00%) | 0.00 | 1.00000 | | Node28 | 1 | >1000 (100.00%) | 2.89 | 0.08859 | | Node10 | 2 | 26.77 ( 7.08%) | 5.72 | 0.02058 | | RYUKYU_MOUSE | 1 | 1.15 (100.00%) | 0.04 | 0.46336 | | Node30 | 1 | 0.17 (100.00%) | 0.00 | 1.00000 | | Node11 | 1 | 0.20 (100.00%) | 0.00 | 1.00000 | | SQUIRREL | 1 | 0.29 (100.00%) | 0.00 | 1.00000 | | Node8 | 1 | 0.61 (100.00%) | 0.00 | 1.00000 | | HOUSE_MOUSE | 1 | 0.78 (100.00%) | 0.00 | 1.00000 | | Node15 | 1 | 0.99 (100.00%) | 0.00 | 1.00000 | | Node19 | 1 | 5.54 (100.00%) | 0.12 | 0.42856 | | MARMOT | 1 | 0.40 (100.00%) | 0.00 | 1.00000 | | Node27 | 1 | 0.23 (100.00%) | 0.00 | 1.00000 | | Node18 | 1 | >1000 (100.00%) | 0.21 | 0.40041 | | Node37 | 1 | >1000 (100.00%) | 1.36 | 0.20027 | ---- ### Adaptive branch site random effects likelihood test Likelihood ratio test for episodic diversifying positive selection at Holm-Bonferroni corrected _p = 0.0500_ found **0** branches under selection among **41** tested.