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 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.