I ran Orthofinder for six plant genomes and got some results, which include a lot of statistics. I only made a phylogenetic tree for those species, but I don't know how to plot other results? How to use those results to do some gene family analyses? Here is the information from the manual:
4.3 Results Files: Orthogroup Statistics The statistics calculated from the orthogroup analysis provide the basis for any comparative genomics analysis. They are easily plotted and can also be used for quality control. Statistics Overall.csv is a tab separated text le giving useful statistics from the orthogroup analysis. Statistics PerSpecies.csv is a tab separated text le giving many of the same statistics as the `Statistics Overall.csv' le but on a species-by-species basis. Orthogroups SpeciesOverlaps.csv is a tab separated text le containing a matrix of the number of orthogroups shared by each species-pair (i.e. the number of orthogroups which contain at least one gene from each of the species-pairs).
Does anybody can help? Thanks in advance.
Best Regards, Zhang