Modified to run on all four species if the species is not specified.

I've also removed the steps for building trees from the non-redundant sequences since they
are in flux
Modified to remove '_cds' from filename from the output when making list of cumulative lengths
Removed functionality to deal with reverse-complemented sequences

These will now be reverse-complemented when added to datasets so I don't have to worry
them when making a list of non-redundant sequences