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.

SEE ALSO

bp-analyze