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 ...
expansions and contractions from OrthoFinder
The input file looks like this, and the complete file can be found here: ...
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 ...
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 ...
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 ...
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 ...