bali-phy1

Usage

Overview

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.

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.

-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.

-t, –test

Analyze the initial values and exit.

-c filename, –config filename

Read commands from filename before command line.

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.

-l arg, –log-format arg

Log-format: tsv or json or tsv,json

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.

Options

-A alphabet, –alphabet alphabet

The alphabet.

-S model, –smodel model

The substitution model.

-I model, –imodel model

The insertion-deletion model.

-R arg, –scale arg

Prior on the scale.

-F arg, –fix arg

Fix topology, tree, or alignment

-L NUMS, –link NUMS

Link partitions. Takes a comma-separated list of numbers indicating partitions. For example --link 1,2,3.

–variables arg

Variable definitions

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.