- Lognormal mixture modeling is implemented for reciprocally retained gene families
- The code supports the use both of lambda rank and of combined rank for rec.ret. data
- To be distinguishable, the files relative to rec.ret. paralogs (i.e. the MCL file and the Ks file) are named after the rank type they are produced from (e.g. lambda)
- The "extra" methods for paralogs analyses have been updated to include LMM on reciprocally retained data