Provided by: phast_1.4+dfsg-1_amd64 
NAME
indelFit - Estimate the parameters of a simple indel model, given an indel history
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).
An indel history can be obtained with indelHistory and a tree with phyloFit.
OPTIONS
--alpha, -a <val>
Starting value of alpha, the insertion rate.
Default is 0.02.
--beta, -b <val> Starting value of beta, the deletion rate. Default is 0.04.
--tau, -t <val> Starting value of tau, the length parameter. Default is 0.05.
--lnl, -L
Compute log likelihood of model only, without optimizing parameters. The options above can be
used to set the parameters as desired.
--columns, -c
Output log likelihood of each column.
--features, -f <file.gff>
Estimate separate parameters for each type of feature in the given file, as well as for background
sites.
--reference, -r <name>
(For use with --features) Name of species (node of tree) defining coordinate frame of features.
By default, the coordinate frame of the entire alignment is assumed.
--log, -l <file>
Write log of optimization to specified file.
--help, -h
Display this help message and exit.