Issue #64 resolved

Add support to homologize for direct orthology identification

Casey Dunn
repo owner created an issue

Rather than identify paralogs phenetically and orthologs phylogenetically, some tools directly identify orthologs phenetically.

One such tool is oma:

http://omabrowser.org/standalone/

We should incorporate oma support within homologize.py. This will require having translations available, as oma only compares proteins.

Downstream analyses can then consist of multalign.py and genetres.py, without the need to run tree prune.py. Although orthologs are identified by protein comparison, matrices can still be constructed by simultaneous alignment and translation.

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