.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH BASE_EVOLVE "1" "May 2016" "base_evolve 1.4" "User Commands"
.SH NAME
base_evolve \- Produce a synthetic alignment by simulating evolution according to
.SH DESCRIPTION
Produce a synthetic alignment by simulating evolution according to
a phylogenetic model or a phylo\-HMM.  Deals with base\-substitution
only, not indels.  If a multiple tree models are given, then an
HMM file must be given showing how to transition between them.
.SH EXAMPLE
.IP
base_evolve \fB\-\-nsites\fR 500 mytree.mod > simulated.fa
.IP
base_evolve \fB\-\-nsites\fR 500 simple\-gene.hmm tree1.mod tree2.mod \e
tree3.mod \fB\-\-features\fR simulated2.gff \fB\-\-catmap\fR simple\-gene.cm \e
> simulated2.fa
.SH OPTIONS
.HP
\fB\-\-nsites\fR, \fB\-n\fR <nsites>
Generate an alignment with <nsites> columns.
Default is 1000.
.HP
\fB\-\-msa\-format\fR, \fB\-o\fR FASTA|PHYLIP|MPM|SS
.TP
Output alignment in specified format.
Default is FASTA.
.HP
\fB\-\-features\fR, \fB\-f\fR <out.gff>
(for use with a phylo\-HMM)
Output an annotations file in GFF
.IP
reflecting the path through the phylo\-HMM.
.HP
\fB\-\-catmap\fR, \fB\-c\fR <map.cm>
.TP
(for use with \fB\-\-features\fR)
Use specified category map to
.IP
define feature names.
.HP
\fB\-\-embed\fR, \fB\-e\fR <alt.mod>,<length>
Embed an artificial element of the given length in the alignment,
drawing columns from <alt.mod>.  A single element is embedded in
the exact middle of the generated alignment.  Useful for testing
sensitivity of methods for functional element detection.
.HP
\fB\-\-help\fR, \fB\-h\fR
.IP
Display this help message and exit.