Question: How to plot Orthofinder results?
gravatar for HZZ0036
2.7 years ago by
HZZ003610 wrote:

Hi everyone,

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. ˆ Statistics Overall.csv is a tab separated text le giving useful statistics from the orthogroup analysis. ˆ 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. ˆ 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

genome • 2.0k views
ADD COMMENTlink modified 2.6 years ago by david_emms110 • written 2.7 years ago by HZZ003610

Hi!! did you find some script to plot the Orthofinder results?


ADD REPLYlink written 20 months ago by imda10
gravatar for david_emms
2.6 years ago by
david_emms110 wrote:

Hi Zhang

There are really hundreds of ways to use the results from OrthoFinder to do all kinds of different analyses, that's the idea! You mention some gene family analyses, can you give some more information about what it is you'd like to investigate about the gene families or what it is you'd like to be able to show with the plots? Hopefully with a few more details of what you're interested in we should be able to give you some suggestions.

All the best


ADD COMMENTlink written 2.6 years ago by david_emms110
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