Understands the "X" symbol
Fewer intermediate structures to list the homologies
Refactored the config files
HMMClassifyCurated is done for all species simultaneously

still to-do: restrict the copy to canonical members ?
HMMClassifyInterpro is done for all species simultaneously

still to-do: restrict the copy to canonical members ?

Intepro annotations are either families or subfamilies
Renamed the runnable to list unannotated members
PantherScore is called by batches instead of genome_db
PantherAnnotation objects are not needed
Option to use non-canonical members in HMMClassify
First version of HMM clustering in the Family pipeline
duplication_confidence_score has to be set later

otherwise it is set to NULL automatically by the for loop
Skip loading the HMMs if possible

Loading all the HMMs (incl. the subfamilies) is quite long. If the
final library is already there, we actually can skip this part, as the
hmm_profile table is never read.
Merged the "allow_pyrrolysine" option under "allow_ambiguity_codes"
4Gb of memory for the HMMClassify factory
TreeBest can also store a default tree
Merge branch 'master' into feature/hmm_classification

* master:
  TreeBest can also store a default tree
  Understands the "X" symbol