.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH INDELFIT "1" "May 2016" "indelFit 1.4" "User Commands"
.SH NAME
indelFit \- Estimate the parameters of a simple indel model, given an indel history
.SH DESCRIPTION
Estimate the parameters of a simple indel model, given an indel history
and a tree.  By default, writes estimates of three parameters to
stdout: an insertion rate alpha, a deletion rate beta, and a parameter
tau roughly equal to the inverse of the expected indel length (modulo
adjustments required to make probabilities sum to one).
.IP
An indel history can be obtained with indelHistory and a tree with
phyloFit.
.SH OPTIONS
.HP
\fB\-\-alpha\fR, \fB\-a\fR <val>
.TP
Starting value of alpha, the insertion rate.
Default is 0.02.
.HP
\fB\-\-beta\fR, \fB\-b\fR <val>
Starting value of beta, the deletion rate.
Default is 0.04.
.HP
\fB\-\-tau\fR, \fB\-t\fR <val>
Starting value of tau, the length parameter.
Default is 0.05.
.HP
\fB\-\-lnl\fR, \fB\-L\fR
.IP
Compute log likelihood of model only, without optimizing parameters.
The options above can be used to set the parameters as desired.
.HP
\fB\-\-columns\fR, \fB\-c\fR
.IP
Output log likelihood of each column.
.HP
\fB\-\-features\fR, \fB\-f\fR <file.gff>
.IP
Estimate separate parameters for each type of feature in the given
file, as well as for background sites.
.HP
\fB\-\-reference\fR, \fB\-r\fR <name>
.IP
(For use with \fB\-\-features\fR) Name of species (node of tree) defining
coordinate frame of features.  By default, the coordinate frame of
the entire alignment is assumed.
.HP
\fB\-\-log\fR, \fB\-l\fR <file>
.IP
Write log of optimization to specified file.
.HP
\fB\-\-help\fR, \fB\-h\fR
.IP
Display this help message and exit.