functionality duplicated by RunPhyml.py
modified to output additional information
Modified to work on Genbank files instead of fasta. I should probably make this an option
add stockholm format as an additional format option
Added info about evalue cutoff to docstring
script now changes all identifiers to lowercase to make comparison case insensitive. I also added a test for blank fields
first commit
Added a test to see if outfile already exists.

This allows a batch of jobs to be stopped, then restarted at a later date without having
to redo the jobs that have already completed