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How to plot Orthofinder results?

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
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updated by david_emms • david_emms • written by HZZ0036 • HZZ0036

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

Ivan

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written by imda • imda

1 answer

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

David

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written by david_emms • david_emms

Hi David I have the same problem. I want to analyse the unassigned genes and single-copy orthologues. One problem is that name of all proteins (from my annotation) are something like (ID_number followed by the gene name. For example: (GCA_000020685.1_ASM2068v1_genomic.fna.fa_00010 Chromosomal replication initiator protein DnaA). Therefore all the proteins in the Orthogroups.tsv file are shown as ID_number : (GCA_000020685.1_ASM2068v1_genomic.fna.fa_00010.fna.fa). How can I have protein names instead of ID_number in my table? My other question is about the analysis of result files. You suggest which tool for analyzing data from unassigned genes and single-copy orthologues files? I am looking for core-genome of species. Best.

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written by Aba.j1987 • Aba.j1987

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