Updates to Genome::families(). Have resolved some of the issues with genes being members of >1 families.
Abstracted sisterSyntenyMatrix out of ohnologComparative2. Useful method so should be standalone. Cleaned up _orthogroup_index().
Minor changes to -quality option for output().
Bug fix in families().
Created Genome::group(-orfs => , -by => x) to manage orfs. Reorged families to use.
Various changes. Added Genome::shape() method. Genomes::families() still has some issues.
Micro changes. Just trying to get a clean repo so I can init gh-pages.