FUBAR

Analysis Description -------------------- Perform a Fast Unbiased AppRoximate Bayesian (FUBAR) analysis of a coding sequence alignment to determine whether some sites have been subject to pervasive purifying or diversifying selection. Please note that a FUBAR analysis generates a cache and a results JSON file in the same directory as directory as the original alignment. HyPhy needs to have write privileges to this directory. For example if the original file is in /home/sergei/FUBAR/data/pol.nex then at the end of a FUBAR run, there will also exist FUBAR-generated files /home/sergei/FUBAR/data/pol.nex.FUBAR.json, /home/sergei/FUBAR/data/pol.nex.fubrar.cache. They also provide checkpointing so that a partially completed analysis can be restarted. - __Requirements__: in-frame codon alignment (possibly partitioned) and a phylogenetic tree (one per partition) - __Citation__: FUBAR: a fast, unconstrained bayesian approximation for inferring selection (2013), Mol Biol Evol. 30(5):1196-205 - __Written by__: Sergei L Kosakovsky Pond - __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/fubar/../../.hyphy/res//TemplateBatchFiles/SelectionAnalyses/`) >Please select a tree file for the data: (`/home/datamonkey/datamonkey-js-test/app/fubar/../../.hyphy/res//TemplateBatchFiles/SelectionAnalyses/`) >Loaded a multiple sequence alignment with **4** sequences, **2757** codons, and **1** partitions from `/home/datamonkey/datamonkey-js-test/app/fubar/output/5b622feca1e50e1b094766de` > FUBAR will write cache and result files to _/home/datamonkey/datamonkey-js-test/app/fubar/output/5b622feca1e50e1b094766de.FUBAR.cache_ and _/home/datamonkey/datamonkey-js-test/app/fubar/output/5b622feca1e50e1b094766de.FUBAR.json_, respectively > Number of grid points per dimension (total number is D^2) (permissible range = [5,50], default value = 20, integer): > Number of MCMC chains to run (permissible range = [2,20], default value = 5, integer): > The length of each chain (permissible range = [500000,50000000], default value = 2000000, integer): > Use this many samples as burn-in (permissible range = [100000,1900000], default value = 1000000, integer): > How many samples should be drawn from each chain (permissible range = [50,1000000], default value = 100, integer): > The concentration parameter of the Dirichlet prior (permissible range = [0.001,1], default value = 0.5): ### Obtaining branch lengths and nucleotide substitution biases under the nucleotide GTR model * Log(L) = -22832.62, AIC-c = 45691.26 (13 estimated parameters) * Tree length (expected substitutions/site) for partition 1 : 0.459 ### Computing the phylogenetic likelihood function on the grid * Determining appropriate tree scaling based on the best score from a 20 x 20 rate grid * Best scaling achieved for * synonymous rate = 7.125 * non-synonymous rate = 0.214 * Computing conditional site likelihoods on a 20 x 20 rate grid ### Running MCMC chains to obtain a posterior sample of (synonymous,non-synonymous) rate weights * Using the following settings * Number of chains : 5 * Steps/chain : 2000000 * Burn-in steps : 1000000 * Samples/chain : 100 * Dirichlet alpha : 0.5 * Running MCMC chain 1 * Running MCMC chain 2 * Running MCMC chain 3 * Running MCMC chain 4 * Running MCMC chain 5