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.

indelFit 1.4                                        May 2016                                         INDELFIT(1)