Man page - bali-phy(1)

Packages contains this manual

Package:  bali-phy
apt-get install bali-phy

Manuals in package:
• alignment-consensus(1)
• cut-range(1)
• alignment-thin(1)
• alignment-max(1)
• bali-phy-pkg(1)
• bp-analyze(1)
• alignment-draw(1)
• summarize-ancestors(1)
• extract-ancestors(1)
• stats-select(1)
• mctree-mean-lengths(1)
• trees-consensus(1)
• alignment-find(1)
• bali-phy(1)
• statreport(1)
• alignment-indices(1)
• tree-mean-lengths(1)
• pickout(1)
• draw-tree(1)
• alignment-gild(1)
• alignment-distances(1)
• alignment-info(1)
• tree-tool(1)
• alignments-diff(1)
• trees-bootstrap(1)
• mcon-tool(1)
• alignment-cat(1)
• alignment-chop-internal(1)
• alignment-translate(1)
• trees-distances(1)
• bali-subsample(1)
Documentations in package:
• bali-phy

Manual

bali-phy

NAME
SYNOPSIS
DESCRIPTION
GENERAL OPTIONS
MCMC OPTIONS
PARAMETER OPTIONS
MODEL OPTIONS
EXAMPLES
REPORTING BUGS
SEE ALSO
AUTHORS

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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 .

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

SEE ALSO

bp-analyze

AUTHORS

Benjamin Redelings.

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