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