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266 Open 634 Closed
266 Open 634 Closed
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Issues list

Test can run "muscle" - failed
#932 opened Oct 29, 2024 by dongyiyi
2
Using scripts to process protein data from NCBI
#930 opened Oct 21, 2024 by wang748
9
ModuleNotFoundError: No module named 'scripts_of'
#928 opened Oct 16, 2024 by caonetto
1
Only 1 gene in HOG in N0.tsv
#926 opened Sep 26, 2024 by sunriseTM
6
-X option
#925 opened Sep 25, 2024 by H1889
Inferring remaining multiple sequence alignments and gene trees——This step has been stuck for ten days
#921 opened Aug 9, 2024 by YuJiang0121
4
disagreement between OrthologuesStats_one-to-one.tsv and Orthogroups.GeneCount.tsv
#920 opened Jul 31, 2024 by shiyi-pan
8
Running OrthoFinder with Large Species Set (>2k)
#919 opened Jul 26, 2024 by BioOmics
9
Option to start Orthofinder at stage of inferring trees from MSAs?
#915 opened Jul 16, 2024 by PollyHannah
1
[Possible Bug] The -og option doesn't stop after inferring orthogroups
#906 opened Jun 16, 2024 by StefanFlaumberg
1
Hello! I have 11 .faa files in a folder. I ran orthofinder -d -f /public/home/newfasta -t 64 -o output_orthofinder. But after 13-14 minutes process failed. There is no error. I opened slurm.out file then checked. there was written like below.
#903 opened Jun 2, 2024 by timurrxxcd
3
"Invalid escape sequence" errors while starting OrthoFinder
#902 opened May 30, 2024 by markusHaferkamp
2
-T raxml-ng——ERROR: Species tree inference failed
#900 opened May 20, 2024 by suncimu
5
Issue with rerunning orthofinder "from trees" step -- Blast0_0.txt not found
#899 opened May 10, 2024 by 00-kelvin
4
Which directories for versions of Orthofinder v2.4.0 (or more recent) are valid with the HOGs?
#898 opened May 10, 2024 by SheepwormJM
ERROR: external program called by OrthoFinder returned an error code: -9
#896 opened May 9, 2024 by zishanw
ValueError: setting an array element with a sequence.
#895 opened Apr 30, 2024 by gsierrar
Identifying number of characters involved in species tree inference using -M msa option
#894 opened Apr 28, 2024 by Fatma116
is it possible to specify a tree for orthofinder?
#893 opened Apr 22, 2024 by AlexGalvez
1
Get order of concatenated sequences in SpeciesTreeAlignment.fa
#892 opened Apr 22, 2024 by SalvadorGJ
Orthogroups vs Superfamily Family Tree
#891 opened Apr 16, 2024 by 000generic
OSError: [Errno 24] Too many open files [32514] Failed to execute script 'orthofinder' due to unhandled exception!
#890 opened Apr 2, 2024 by MassimoCasagranda
DockerFile
#888 opened Mar 28, 2024 by TheLillo
Only two species comparison, but the number of one-to-one orthologs in Orthologues Stats one_to_one.tsv is more than the number of single-copy orthogroups in statistics Overall.tsv file
#887 opened Mar 25, 2024 by HyCipher
Is it possible to detect Orthologous Isoforms
#886 opened Mar 18, 2024 by Tang-pro
ProTip! Find all open issues with in progress development work with linked:pr.