PROGRAM: indelFit

USAGE: indelFit [OPTIONS] indel-history.ih tree.nh > out

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.