Right now the E-value cutoff is 1E-5. It's been fine for our purposes but people might want to go lower than that... we can just make it an optional parameter in the script.
Fixed, tested, works, committed. These E-values are now options in the main.sh script. The defaults are identical to what they were before (1E-5 for BLASTP and 1.0 for BLASTN).
Right now the E-value cutoff is 1E-5. It's been fine for our purposes but people might want to go lower than that... we can just make it an optional parameter in the script.