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.