Added QUALITY attribute to accelerate ->quality()
Changed  _score_syntenic_alignment() to score orthologous as well as a paralogous alignments.
Changed syntenyMatrix to synteny_matrix() and restructured to three run modes: unaligned (synteny_conserved), ortholog, paralog. The latter use dpalign() before applying a scoring matrix but for backward consistency the default is "nonaligned". Also a bunch of other changes I have not been tracking properly. High risk of breakign stuff..
Created diagnose() method to identify weakest member of an orthogroup. Performs N multiple alignments around the OG members with N-1 members each time. Dropping out the problem should boost the score. Assumes a single problem member but a reasonable start. Can cross tablulate with sowh and other methods to isolate and correct inaccurate OGs.
Made a bunch of ridiculous changes to phyml() to get the sowh() method working again. I think I have a very old version of Phyml installed and update was a mess.
Updated synteic_alignment() to make it more rigorous and explicit. Can now do syntenic alignment without enforcing ancestor. Also created ancestral_alignment() wrapper.
Debugging.
Tightening up  synteny_matrix.
Modified error checking in hmmer3.
Modified parser for hmmer3().
Minor changes to update().
Minor changes.
Phyml() added -molecule argument to allow protein trees.
Phyml() more minor changes.
Minor changes in synteny_matrix().
Minor.
Minor changes in synteny_matrix(). Conversion of score to distance.
Created     my %distance =
Debugging changes.
Changes to paml() to handle yn00 properly (treefile).