NAME

bali-phy - Bayesian Inference of Alignment and Phylogeny

SYNOPSIS

bali-phy sequence-file1 [sequence-file2 ...] [OPTIONS]

bali-phy help topic

DESCRIPTION

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.

GENERAL OPTIONS

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.

MCMC OPTIONS

-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.

PARAMETER OPTIONS

-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.

MODEL OPTIONS

-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.

EXAMPLES

bali-phy dna.fasta --smodel gtr: Analyze sequences in dna.fasta under the GTR model.
bali-phy dna.fasta -S 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:lg08 -S 3:gy94: 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.

REPORTING BUGS

BAli-Phy online help: <http://www.bali-phy.org/docs.php>.

Please send bug reports to <bali-phy-users@googlegroups.com>.

AUTHORS

Benjamin Redelings.