DOKK / manpages / debian 11 / bali-phy / bali-phy.1.en
bali-phy(1) bali-phy(1)

bali-phy - Bayesian Inference of Alignment and Phylogeny

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

bali-phy help topic

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.

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

Display a friendly help message. Specify --help=advanced or --help=expert to display more advanced options.
Print version information.
Analyze the initial values and exit.
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.
Read commands from filename before command line.

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.

File with initial tree in Newick format or NEXUS format.
Unalign all variable-alignment partitions before starting MCMC instead using the supplied alignment as a starting value.

The alphabet.
The substitution model.
The insertion-deletion model.
Prior on branch lengths.
Prior on the scale.
Link partitions. Takes a comma-separated list of numbers indicating partitions. For example --link 1,2,3.

Analyze sequences in dna.fasta under the GTR model.
Perform a traditional fixed-alignment analysis with gaps treated as missing data.
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.

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

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

bp-analyze

Benjamin Redelings.

Feb 2018