.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH INDELHISTORY "1" "May 2016" "indelHistory 1.4" "User Commands"
.SH NAME
indelHistory \- Obtain an "indel history" for an alignment and write it to a file
.SH DESCRIPTION
Obtain an "indel history" for an alignment and write it to a file
describing insertions and deletions in all species using a compact
format.  The specified alignment may either contain sequences
corresponding only to leaves of the specified tree, in which case an
indel history will be inferred using a simple parsimony algorithm, or
it may contain sequences for all nodes in the tree, in which case the
indel history will simply be extracted from the file.
.SH OPTIONS
.HP
\fB\-\-msa\-format\fR, \fB\-i\fR FASTA|MAF|SS|....
.IP
Read alignment in specified file format (default FASTA).
.HP
\fB\-\-output\-alignment\fR, \fB\-A\fR
.IP
Instead of a summary of indels only, output an alignment in FASTA
format of sequences for all ancestral and leaf nodes.
.HP
\fB\-\-read\-history\fR, \fB\-H\fR <fname>
Read an indel history directly from the specified file.
Useful for
debugging.
The alignment and tree arguments are not required;
.IP
however in an alignment is given with \fB\-\-read\-history\fR and
\fB\-\-output\-alignment\fR, then actual bases can be output for leaf
species.
.HP
\fB\-\-ia\-names\fR, \fB\-I\fR
.IP
Assume ancestral sequences in alignment.fa are named according to
the convention used by Mathieu Blanchette's inferAncestors program,
e.g., "RAT+MOUSE+RABBIT+" for the last common ancestor of "rat",
"mouse", and "rabbit".
.HP
\fB\-\-help\fR, \fB\-h\fR
.IP
Display this help message.