added Getopt::Long command line argument parsing, now attempts to translate sequences to AA locally without recourse to GenBank if no accession number can be parsed out, emits a warning when doing so
added Getopt::Long command line argument handling
adding shell script wrapper for pipeline
removed extraneous -as_project argument to parse_matrix
adding ACS1&2 data files
made command line arguments more specific, added protein alignment and nuc-to-protein alignment steps