added make_codeml script, and removed extra shit
Merge pull request #1 from jwayne/lawrence

added make_codeml script, and removed extra shit
added basic preprocessing code
Merge pull request #2 from jwayne/josh

(for lawrence) added basic preprocessing code
missed a comma
Merge pull request #3 from jwayne/josh

missed a comma
added some shit
Added ctl generator to process.py. Updated bins+makefile.
Merge pull request #4 from jwayne/lawrence

added some shit
Added ctl generator to process.py. Updated bins+makefile.
progress on input handling
rebase conflict
Merge pull request #5 from jwayne/josh

added idea, progress on input file parsing
renamed jlj -> src
Merge pull request #6 from jwayne/lawrence

renamed jlj -> src
progress on input preprocessing
fixed lawrence's duplicate issue
Merge pull request #7 from jwayne/josh

progress on input preprocessing
batch searches protein and nucleotide separately
translates nucleotide to amino acids