Moved code from syntenic_paralogs() tp Orf.pm and replaced old - terrible - sisters() code. Returns an array of candidate sister regions as [Orf, AncLocus].
Created Orf::density() wrapper around ancestralSyntenyDensity() to facilitate access to only the scaled (0-1) value.
Cleaned up  syntenic_paralogs(). ALternatives handled properly.
Minor debug.
Minor debug.
Added more intelligent selection of sister candidates to indexCandidateSisterRegions(). Not fully working/tested.
Documentation improvements in indexCandidateSisterRegions() to enable debugging.
Squashed bug in indexCandidateSisterRegions(). No longer missing high quality candidates.
Added simple method to analyze alignments and score various aspects _testOhnoSpan().
Made changes in syntenic_paralogs() to allow more consistent comparisons of alternate hypotheses to proposed ohnolog pair. Added checks to ensure alt hypotheses are valid (i.e. not being mislead by rearrangements).
Minor tweaks.
Minor tweaks.