Changed --abundance-threshold to --minimum-abundance for clarity.
Major revision.  Added 454 support, moving it to the front of the pipeline for pre-filtering as opposed to post-filtering.  It now will sum abundances of lesser abundant sequences differing from more abundant sequences only by indels.
Changed --abundance-threshold to --minimum-abundance for clarity.
Changed --abundance-threshold to --minimum-abundance for clarity.  Deleted old commented lines.
Changed --abundance-threshold to --minimum-abundance for clarity.
Added required modules for the new filterIndels.pl functionality (454 support).
Changed the documentation to reflect added 454 functionality.
Upped the IO::Pipe::Producer version requirement.
New wrapper script for running the pipeline on 454 data.