Provided by: bali-phy_3.3+dfsg-1_amd64
bali-phy – Bayesian Alignment and Phylogeny estimation using MCMC
bali-phy sequence-file1 [sequence-file2 ...] [OPTIONS] bali-phy help topic
bali-phy estimates multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences. BAli-Phy uses MCMC and Bayesian methods to estimate evolutionary trees, positive selection, and branch lengths while averaging over alternative alignments. BAli-Phy can also estimate phylogenies from a fixed alignment (like MrBayes and BEAST) using substitution models like GTR+gamma. BAli-Phy automatically estimates relative rates for each gene.
For each option below, more information is available by specifying the long form of the option as a help topic. For example: bali-phy help alphabet -h, –help, –help=topic Display a friendly help message. Specify –help=advanced or –help=expert to display more advanced options. -v, –version Print version information. -t, –test Analyze the initial values and exit. -V, –verbose, –verbose NUM Print extra output to aid in trouble-shooting. If NUM is not specified the default is 1. Values from 2 to 4 increase the amount of information displayed. -c filename, –config filename Read commands from filename before command line.
-i NUM, –iterations NUM The number of iterations to run. -n STRING, –name STRING Name for the output directory to create. -x NUM, –subsample NUM Factor by which to subsample. This option should usually not be used. -s NUM, –seed NUM Random seed. Useful for replaying specific runs when trouble-shooting.
-T filename, –tree filename File with initial tree in Newick format or NEXUS format. -U, –unalign Unalign all variable-alignment partitions before starting MCMC instead using the supplied alignment as a starting value.
-A alphabet, –alphabet alphabet The alphabet. -S model, –smodel model The substitution model. -I model, –imodel model The insertion-deletion model. -B prior, –branch-lengths prior Prior on branch lengths. -R prior, –scale prior Prior on the scale. -L NUMS, –link NUMS Link partitions. Takes a comma-separated list of numbers indicating partitions. For example –link 1,2,3.
bali-phy dna.fasta –smodel GTR Analyze sequences in dna.fasta under the GTR model. bali-phy dna.fasta –smodel GTR -I none Perform a traditional fixed-alignment analysis with gaps treated as missing data. bali-phy dna.fasta amino.fasta codons.fasta -S 1:GTR -S 2:LG -S 3:M0 Perform an analysis of 3 genes where each gene has a different substitution mode. The sequence names in all three files must be the same.
BAli-Phy online help: <http://www.bali-phy.org/docs.php>. Please send bug reports to <firstname.lastname@example.org>.
Benjamin Redelings. Feb 2018 bali-phy(1)