Answers.Body: <p>I think they simply calculate the percentage of proteins in each species that belongs to an orthogroup conserved in the five species.</p>
  <p>There should be a tab separated text file called Orthogroups.GeneCount.tsv (at least in the Orthofinder version used in the paper). This file contains counts of the number of genes for each species in each orthogroup. You can use this file to get the total number of genes in each species associated with those 7950 orthogroups and then calculate its proportion compared to the total number of genes.</p>
  <p>Hope this helps</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-12-19T11:58:39.677Z
Answers.LastActivityDate: 2022-12-19T11:58:39.677Z
Answers.UserDisplayName: CorteZero
Body: <p>I read this paper (<em>Colletotrichum shisoi sp. nov., an anthracnose pathogen of Perilla frutescens in Japan: molecular phylogenetic, morphological and genomic evidence</em>). We ran Orthofinder and also created an Upset plot. Unfortunately, I do not understand how they calculated the following percentages in the <em>&quot;Conservation of proteins amongst Colletotrichum species&quot;</em> section:</p>
  <blockquote>
  <p>A total of 11,914 orthogroups with two or more proteins were
  identified (Fig. 4b). Of these, 7,950 groups (74.0% proteins from C.
  shisoi, 63.0% from C. higginsianum, 78.3% from C. incanum, 74.2% from
  C. tofieldiae and 73.7% from C. graminicola) were conserved in all
  five species (Supplementary Tables S3 and S4)</p>
  </blockquote>
  <p>How is it possible to calculate the values?</p>
  <p>Thank you in advance</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-12-19T12:56:51.513Z
Comments.Text: Ah this is a core-genome calculation. Very interesting study indeed. Agreed its not clear but I think @CorteZero has the right idea.
Comments.UserDisplayName: M__
Tags: <clustering><orthologues><clusterprofiler><orthofinder>
Title: How to analyse Orthofinder results
ThreadText: # How to analyse Orthofinder results
  
  (Asked by: username_0 on 2022-12-19)
  
  I read this paper (*Colletotrichum shisoi sp. nov., an anthracnose pathogen of Perilla frutescens in Japan: molecular phylogenetic, morphological and genomic evidence*). We ran Orthofinder and also created an Upset plot. Unfortunately, I do not understand how they calculated the following percentages in the *"Conservation of proteins amongst Colletotrichum species"* section:
  
  > A total of 11,914 orthogroups with two or more proteins were
  > identified (Fig. 4b). Of these, 7,950 groups (74.0% proteins from C.
  > shisoi, 63.0% from C. higginsianum, 78.3% from C. incanum, 74.2% from
  > C. tofieldiae and 73.7% from C. graminicola) were conserved in all
  > five species (Supplementary Tables S3 and S4)
  
  How is it possible to calculate the values?
  
  Thank you in advance
  
  **Tags:** clustering, orthologues, clusterprofiler, orthofinder
  
  > **Comments:**
  > **username_1**: Ah this is a core-genome calculation. Very interesting study indeed. Agreed its not clear but I think @username_2 has the right idea.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2022-12-19. Score: 4
  
  I think they simply calculate the percentage of proteins in each species that belongs to an orthogroup conserved in the five species.
  
  There should be a tab separated text file called Orthogroups.GeneCount.tsv (at least in the Orthofinder version used in the paper). This file contains counts of the number of genes for each species in each orthogroup. You can use this file to get the total number of genes in each species associated with those 7950 orthogroups and then calculate its proportion compared to the total number of genes.
  
  Hope this helps
  
  
  ---
  
  