NAME

       indelHistory - Obtain an "indel history" for an alignment and write it to a file

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.