Update MLSSIDFactory.pm

Runs dNdS for homoeologues as well
Update EGPairAligner_conf.pm

bidirectional netting is now the default for Ensembl Genomes, so set it to 1.
Merge commit 'refs/pull/github/10'

* commit 'refs/pull/github/10':
  Update EGPairAligner_conf.pm
  Update MLSSIDFactory.pm

Conflicts:
	modules/Bio/EnsEMBL/Compara/RunnableDB/ProteinTrees/MLSSIDFactory.pm