---
name: "bali-phy"
section: "1"
platform: "linux"
package: "bali-phy"
version: "4.0-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bali-phy"
---

# bali-phy(1)

Bayesian Inference of Alignment and Phylogeny

## 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.

- **-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.

## 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.

- **-l** *arg*, **–log-format** *arg*

  Log-format: `tsv` or `json` or `tsv,json`

## 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.

- **-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.

## REPORTING BUGS

BAli-Phy online help: ⟨http://www.bali-phy.org/docs.php⟩\\c .

Please send bug reports to ⟨bali-phy-users@googlegroups.com⟩\\c .

## SEE ALSO

bp-analyze

## AUTHORS

Benjamin Redelings.