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.