fixed stupid errors in preprocessing
Merge pull request #11 from jwayne/lawrence

(for Josh) wrote fetch homologs by using qblast on blastn
Merge pull request #12 from jwayne/josh

fixed stupid errors in preprocessing
pal2nal works, as does nucleotide conversion :)
push what i have
Merge pull request #13 from jwayne/josh

Singlerun works.
remove ipdb
Merge pull request #14 from jwayne/josh

remove ipdb
codonml.ctl ==> codonml_template.ctl