1) Install instructions missing!
It may be basic to even a linux beginner, but we all remember our first install experience... We need to have some instructions on how to untar / unzip / make and install the package.

2) Results file description missing!
fomat of results file should be described, and results file parser included. Would Uniprot give us their nice XML format parser?

3) Parameters not described fully!
we need to parasie the original research papers.

4) Not much is said about why cd-hit and mcd-hit are included in the distribution.

5) I should add my perl function for picking wordlength and program given a sequence identity threshold.