Questions tagged [orthofinder]

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Given a FASTA file with a set of genes, how do I determine that set's conservation among a genetic order?

Given a set of genes in a FASTA-formatted file, for example: exFasta.fa, what is the best way to determine how well conserved the genes in that file are among an ...
  • 11
2 votes
2 answers

expansions and contractions from OrthoFinder

The input file looks like this, and the complete file can be found here: ...
3 votes
1 answer

How to analyse Orthofinder results

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 ...
2 votes
1 answer

No bootstrap value on single-copy gene tree created by OrthoFinder

I'm running analysis with OrthoFinder and it produces a single-copy gene tree. When I visualize the tree with iTOL, there's no bootstrap value on the branches or nodes. There's a published paper in ...
  • 121
1 vote
1 answer

Number of sing-copy genes identified by orthofinder is far less than BUSCO assessment?

Dear Orthofinder users and BUSCO users, Recently, I have assessed 30 genome annotataions using BUSCO with lineage dataset ...
  • 81
0 votes
1 answer

Removing data from OrthoFinder output prefix

I am using OrthoFinder to find orthogroups between species. I am using the latest version unpacked through tar as per their instructions. Orthofinder creates an output folder according to the current ...