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Hello David,
I am trying to run OrthoFinder (version 2.5.4), but after several attempts it fails with same error:
Best outgroup(s) for species tree
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2021-07-11…
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yeast DEF1 is currently annotated to transcription-coupled nucleotide-excision repair.
However,
pmid:23993092
"Like DNA replication, transcription is severely affected by DNA damage, with various…
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Dear David,
I installed Orthofinder v2.5.4 via conda, however, when I run the ExampleData, I get the following error:
OrthoFinder version 2.5.4 Copyright (C) 2014 David Emms
2022-08-11 10:01:…
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Basic example (provided by Anushya):
http://panthertest2.usc.edu/services/ortholog/matchOrtho.jsp?format=json&organism=9606&targetOrganism=10090,9913,83333&geneInputList=brca1&orthologType=all
I…
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Hi,
I want to run OrthoFinder from the Gene Trees step onwards. The reason is that I am only interested in the duplication history of a subset of orthogroups. However the default of OrthoFinder is …
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Input: set of gene names, species tree?
Internally:
- fetch species absence/presence vector for each gene
- prune species tree or dim leaves with no genes
- schematically draw genes using different c…
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I find that the "Number of blastp hits with different percentage identity" presented in p.5 of the output file Rplots.pdf could be a simple useful tool to estimate the blastp threshold to use to consi…
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Hi, I'm having a problem running orthofinder, it seems to quit after starting to calculating gene distances without giving the normal output. I'm certain all programs are installed and running correct…
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...
2021-03-13 16:16:44 : Written final scores for species 117 to graph file
2021-03-13 16:16:45 : Written final scores for species 110 to graph file
2021-03-13 16:16:45 : Written final scores fo…
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Hi, I want to use OrthoFinder to study orthology relationships for all genes in multiple species.
I ran orthofinder with the command : orthofinder -f prot
and got this error:
Traceback (most rece…