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.TH "bali-phy" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]bali-phy\f[R] - Bayesian Inference of Alignment and Phylogeny
.SH SYNOPSIS
.PP
\f[B]bali-phy\f[R] \f[I]sequence-file1\f[R] [\f[I]sequence-file2\f[R]
\&...]
[\f[I]OPTIONS\f[R]]
.PP
\f[B]bali-phy\f[R] help \f[I]topic\f[R]
.SH DESCRIPTION
.PP
\f[B]bali-phy\f[R] 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.
.PP
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.
.SH GENERAL OPTIONS
.PP
For each option below, more information is available by specifying the
long form of the option as a help topic.
For example: \f[V]bali-phy help alphabet\f[R]
.TP
\f[B]-h\f[R], \f[B]--help\f[R], \f[B]--help\f[R]=\f[I]topic\f[R]
Display a friendly help message.
Specify \f[B]--help=advanced\f[R] or \f[B]--help=expert\f[R] to display
more advanced options.
.TP
\f[B]-v\f[R], \f[B]--version\f[R]
Print version information.
.TP
\f[B]-t\f[R], \f[B]--test\f[R]
Analyze the initial values and exit.
.TP
\f[B]-V\f[R], \f[B]--verbose\f[R], \f[B]--verbose\f[R] \f[I]NUM\f[R]
Print extra output to aid in trouble-shooting.
If \f[I]NUM\f[R] is not specified the default is 1.
Values from 2 to 4 increase the amount of information displayed.
.TP
\f[B]-c\f[R] \f[I]filename\f[R], \f[B]--config\f[R] \f[I]filename\f[R]
Read commands from \f[I]filename\f[R] before command line.
.SH MCMC OPTIONS
.TP
\f[B]-i\f[R] \f[I]NUM\f[R], \f[B]--iterations\f[R] \f[I]NUM\f[R]
The number of iterations to run.
.TP
\f[B]-n\f[R] \f[I]STRING\f[R], \f[B]--name\f[R] \f[I]STRING\f[R]
Name for the output directory to create.
.TP
\f[B]-x\f[R] \f[I]NUM\f[R], \f[B]--subsample\f[R] \f[I]NUM\f[R]
Factor by which to subsample.
This option should usually not be used.
.TP
\f[B]-s\f[R] \f[I]NUM\f[R], \f[B]--seed\f[R] \f[I]NUM\f[R]
Random seed.
Useful for replaying specific runs when trouble-shooting.
.SH PARAMETER OPTIONS
.TP
\f[B]-T\f[R] \f[I]filename\f[R], \f[B]--tree\f[R] \f[I]filename\f[R]
File with initial tree in Newick format or NEXUS format.
.TP
\f[B]-U\f[R], \f[B]--unalign\f[R]
Unalign all variable-alignment partitions before starting MCMC instead
using the supplied alignment as a starting value.
.SH MODEL OPTIONS
.TP
\f[B]-A\f[R] \f[I]alphabet\f[R], \f[B]--alphabet\f[R] \f[I]alphabet\f[R]
The alphabet.
.TP
\f[B]-S\f[R] \f[I]model\f[R], \f[B]--smodel\f[R] \f[I]model\f[R]
The substitution model.
.TP
\f[B]-I\f[R] \f[I]model\f[R], \f[B]--imodel\f[R] \f[I]model\f[R]
The insertion-deletion model.
.TP
\f[B]-B\f[R] \f[I]prior\f[R], \f[B]--branch-lengths\f[R] \f[I]prior\f[R]
Prior on branch lengths.
.TP
\f[B]-R\f[R] \f[I]prior\f[R], \f[B]--scale\f[R] \f[I]prior\f[R]
Prior on the scale.
.TP
\f[B]-L\f[R] \f[I]NUMS\f[R], \f[B]--link\f[R] \f[I]NUMS\f[R]
Link partitions.
Takes a comma-separated list of numbers indicating partitions.
For example \f[V]--link 1,2,3\f[R].
.SH EXAMPLES
.TP
\f[V]bali-phy dna.fasta --smodel gtr\f[R]
Analyze sequences in \f[I]dna.fasta\f[R] under the GTR model.
.TP
\f[V]bali-phy dna.fasta -S gtr -I none\f[R]
Perform a traditional fixed-alignment analysis with gaps treated as
missing data.
.TP
\f[V]bali-phy dna.fasta amino.fasta codons.fasta -S 1:gtr -S 2:lg08 -S 3:gy94\f[R]
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.
.SH REPORTING BUGS
.PP
BAli-Phy online help: <http://www.bali-phy.org/docs.php>.
.PP
Please send bug reports to <bali-phy-users@googlegroups.com>.
.SH SEE ALSO
.PP
bp-analyze
.SH AUTHORS
Benjamin Redelings.