Questions tagged [orthofinder]
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6
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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 ...
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votes
2
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expansions and contractions from OrthoFinder
The input file looks like this, and the complete file can be found here:
...
- 165
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answer
165
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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 ...
- 165
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1
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114
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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
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82
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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
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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 ...
