bali-phy1
Bayesian inference of alignment and phylogeny
Usage
bali-phy sequence-file1
[sequence-file2 ...]
[OPTIONS]
bali-phy help
topic
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=advancedor–help=expertto display more advanced options.
-v,–version-
Print version information.
-V,–verbose,–verboseNUM-
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.
-cfilename,–configfilename-
Read commands from filename before command line.
Options
|
The number of iterations to run. |
|---|---|
|
Name for the output directory to create. |
|
Factor by which to subsample. This option should usually not be used. |
|
Random seed. Useful for replaying specific runs when trouble-shooting. |
|
Log-format: |
Options
-Tfilename,–treefilename-
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
-Aalphabet,–alphabetalphabet-
The alphabet.
-Smodel,–smodelmodel-
The substitution model.
-Imodel,–imodelmodel-
The insertion-deletion model.
-Rarg,–scalearg-
Prior on the scale.
-Farg,–fixarg-
Fix topology, tree, or alignment
-LNUMS,–linkNUMS-
Link partitions. Takes a comma-separated list of numbers indicating partitions. For example
--link 1,2,3.
–variablesarg-
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.
Releases
4 releases since Debian 10 (Buster); the text changed 2 times.
--alphabet until Debian 12 (Bookworm);
--branch-lengths until Debian 12 (Bookworm);
--config until Debian 12 (Bookworm);
--help until Debian 12 (Bookworm);
--imodel until Debian 12 (Bookworm);
--iterations until Debian 12 (Bookworm);
--link until Debian 12 (Bookworm);
--name until Debian 12 (Bookworm);
--scale until Debian 12 (Bookworm);
--seed until Debian 12 (Bookworm);
--smodel until Debian 12 (Bookworm);
--subsample until Debian 12 (Bookworm);
--test until Debian 12 (Bookworm);
--tree until Debian 12 (Bookworm);
--unalign until Debian 12 (Bookworm);
--verbose until Debian 12 (Bookworm);
--version until Debian 12 (Bookworm);
-A until Debian 12 (Bookworm);
-B until Debian 12 (Bookworm);
-I until Debian 12 (Bookworm);
-L until Debian 12 (Bookworm);
-R until Debian 12 (Bookworm);
-S until Debian 12 (Bookworm);
-T until Debian 12 (Bookworm);
-U until Debian 12 (Bookworm);
-V until Debian 12 (Bookworm);
-c until Debian 12 (Bookworm);
-h until Debian 12 (Bookworm);
-i until Debian 12 (Bookworm);
-n until Debian 12 (Bookworm);
-s until Debian 12 (Bookworm);
-t until Debian 12 (Bookworm);
-v until Debian 12 (Bookworm);
-x until Debian 12 (Bookworm).