PROGRAM: indelHistory

USAGE: indelHistory [OPTIONS] alignment.fa tree.mod > out.ih

DESCRIPTION:

    Obtain an "indel history" for an alignment and write it to a file
    describing insertions and deletions in all species using a compact
    format.  The specified alignment may either contain sequences
    corresponding only to leaves of the specified tree, in which case an
    indel history will be inferred using a simple parsimony algorithm, or
    it may contain sequences for all nodes in the tree, in which case the
    indel history will simply be extracted from the file.

OPTIONS:
    --msa-format, -i FASTA|MAF|SS|....
        Read alignment in specified file format (default FASTA).

    --output-alignment, -A
        Instead of a summary of indels only, output an alignment in FASTA
        format of sequences for all ancestral and leaf nodes.

    --read-history, -H <fname>
        Read an indel history directly from the specified file.  Useful for
        debugging.  The alignment and tree arguments are not required;
        however in an alignment is given with --read-history and
        --output-alignment, then actual bases can be output for leaf
        species.

    --ia-names, -I
        Assume ancestral sequences in alignment.fa are named according to
        the convention used by Mathieu Blanchette's inferAncestors program,
        e.g., "RAT+MOUSE+RABBIT+" for the last common ancestor of "rat",
        "mouse", and "rabbit".

    --help, -h
        Display this help message.