/HYPHY 2.3.1120180218beta(MP) for Darwin on x86_64\ ***************** TYPES OF STANDARD ANALYSES ***************** (1) Selection Analyses (2) Evolutionary Hypothesis Testing (3) Relative evolutionary rate inference (4) Basic Analyses (5) Codon Selection Analyses (6) Compartmentalization (7) Data File Tools (8) Miscellaneous (9) Model Comparison (10) Kernel Analysis Tools (11) Molecular Clock (12) Phylogeny Reconstruction (13) Positive Selection (14) Recombination (15) Selection/Recombination (16) Relative Rate (17) Relative Ratio (18) Substitution Rates Please select type of analyses you want to list (or press ENTER to process custom batch file):1 ***************** FILES IN 'Selection Analyses' ***************** (1) [MEME] Test for episodic site-level selection using MEME (Mixed Effects Model of Evolution). (2) [FEL] Test for pervasive site-level selection using FEL (Fixed Effects Likelihood). (3) [SLAC] Test for pervasive site-level selection using SLAC (Single Likelihood Ancestor Counting). (4) [FUBAR] Test for pervasive site-level selection using FUBAR (Fast Unconstrained Bayesian AppRoximation for inferring selection). (5) [BUSTED] Test for episodic gene-wide selection using BUSTED (Branch-site Unrestricted Statistical Test of Episodic Diversification). (6) [aBSREL] Test for lineage-specific evolution using the branch-site method aBS-REL (Adaptive Branch-Site Random Effects Likelihood). (7) [RELAX] Test for relaxation of selection pressure along a specified set of test branches using RELAX (a random effects test of selection relaxation). Please select the analysis you would like to perform (or press ENTER to return to the list of analysis types):1 Analysis Description -------------------- MEME (Mixed Effects Model of Evolution) estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and uses a likelihood ratio test to determine if β+ > α at a site. The estimates aggregate information over a proportion of branches at a site, so the signal is derived from episodic diversification, which is a combination of strength of selection [effect size] and the proportion of the tree affected. 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__: Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764. - __Written by__: Sergei L. Kosakovsky Pond, Steven Weaver - __Contact Information__: spond@temple.edu - __Analysis Version__: 2.0.1 ####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):1 >Select a coding sequence alignment file (`/Users/tim/Source/git/hyphy/res/TemplateBatchFiles/SelectionAnalyses/`) new3_4.3.4_elaterid_luciferase_nucleotide_nostop.msa.fas >Please select a tree file for the data: (`/Users/tim/Source/git/hyphy/res/TemplateBatchFiles/SelectionAnalyses/`) aBSREL_produced_tree.newick.txt >Loaded a multiple sequence alignment with **20** sequences, **553** codons, and **1** partitions from `/Users/tim/Source/git/hyphy/res/TemplateBatchFiles/SelectionAnalyses/new3_4.3.4_elaterid_luciferase_nucleotide_nostop.msa.fas` ####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 36 unlabeled branches 5. [**Foreground**] Set Foreground with 1 branches >Please choose an option (or press q to cancel selection):5 >Select the p-value threshold to use when testing for selection (permissible range = [0,1], default value = 0.1): ### Branches to include in the MEME analysis Selected 1 branches to include in the MEME analysis: `Node4` ### Obtaining branch lengths and nucleotide substitution biases under the nucleotide GTR model * Log(L) = -16889.13, AIC-c = 33868.39 (45 estimated parameters) ### Obtaining the global omega estimate based on relative GTR branch lengths and nucleotide substitution biases * Log(L) = -15963.98, AIC-c = 32034.48 (53 estimated parameters) * non-synonymous/synonymous rate ratio for *background* = 0.1927 * non-synonymous/synonymous rate ratio for *test* = 0.7229 ### Improving branch lengths, nucleotide substitution biases, and global dN/dS ratios under a full codon model * Log(L) = -15963.98 * non-synonymous/synonymous rate ratio for *background* = 0.1924 * non-synonymous/synonymous rate ratio for *test* = 0.7268 ### For partition 1 these sites are significant at p <=0.1 | Codon | Partition | alpha | beta+ | p+ | LRT |Episodic selection detected?| # branches | |:----------:|:----------:|:----------:|:----------:|:----------:|:----------:|:--------------------------:|:----------:| | 34 | 1 | 0.466 | 23.467 | 1.000 | 4.091 | Yes, p = 0.0603 | 0 | | 46 | 1 | 0.000 | 3.010 | 1.000 | 4.512 | Yes, p = 0.0485 | 0 | | 49 | 1 | 0.933 | 792.389 | 1.000 | 3.828 | Yes, p = 0.0692 | 0 | | 50 | 1 | 0.570 | 3332.294 | 1.000 | 4.760 | Yes, p = 0.0427 | 0 | | 72 | 1 | 0.554 | 3333.111 | 1.000 | 3.128 | Yes, p = 0.0998 | 0 | | 105 | 1 | 0.443 | 6.849 | 1.000 | 4.275 | Yes, p = 0.0549 | 0 | | 118 | 1 | 0.298 | 3333.111 | 1.000 | 7.425 | Yes, p = 0.0109 | 1 | | 146 | 1 | 0.336 | 12.766 | 1.000 | 4.936 | Yes, p = 0.0390 | 0 | | 147 | 1 | 0.751 | 3333.556 | 1.000 | 5.913 | Yes, p = 0.0236 | 0 | | 226 | 1 | 1.440 | 29.623 | 1.000 | 4.760 | Yes, p = 0.0427 | 0 | | 234 | 1 | 1.132 | 9.571 | 1.000 | 3.141 | Yes, p = 0.0991 | 0 | | 290 | 1 | 0.919 | 3333.022 | 1.000 | 3.978 | Yes, p = 0.0640 | 0 | | 315 | 1 | 0.689 | 29.522 | 1.000 | 5.081 | Yes, p = 0.0362 | 0 | | 337 | 1 | 0.262 | 13.317 | 1.000 | 6.255 | Yes, p = 0.0198 | 0 | | 365 | 1 | 0.577 | 7.566 | 1.000 | 4.376 | Yes, p = 0.0520 | 0 | | 369 | 1 | 0.209 | 6.781 | 1.000 | 6.559 | Yes, p = 0.0169 | 0 | | 383 | 1 | 0.000 | 2.827 | 1.000 | 4.121 | Yes, p = 0.0594 | 0 | | 398 | 1 | 0.955 | 1999.200 | 1.000 | 4.454 | Yes, p = 0.0500 | 0 | | 406 | 1 | 0.577 | 5.501 | 1.000 | 3.685 | Yes, p = 0.0745 | 0 | | 423 | 1 | 0.667 | 1574.575 | 1.000 | 4.745 | Yes, p = 0.0430 | 0 | | 432 | 1 | 0.000 | 2.865 | 1.000 | 3.127 | Yes, p = 0.0999 | 1 | | 441 | 1 | 1.434 | 39.278 | 1.000 | 4.190 | Yes, p = 0.0573 | 0 | | 478 | 1 | 0.000 | 10.340 | 1.000 | 6.942 | Yes, p = 0.0139 | 1 | | 502 | 1 | 0.501 | 1790.435 | 1.000 | 4.920 | Yes, p = 0.0393 | 0 | | 528 | 1 | 0.000 | 2.203 | 1.000 | 3.618 | Yes, p = 0.0772 | 0 | | 541 | 1 | 0.000 | 1999.200 | 1.000 | 10.393 | Yes, p = 0.0024 | 1 | | 542 | 1 | 0.560 | 68.036 | 1.000 | 6.267 | Yes, p = 0.0197 | 0 | | 550 | 1 | 0.743 | 3332.911 | 1.000 | 4.302 | Yes, p = 0.0541 | 0 | ### ** Found _28_ sites under episodic diversifying positive selection at p <= 0.1** Check errors.log for details on execution errors. Check messages.log details of this run.