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Issues list

-T raxml-ng——ERROR: Species tree inference failed
#900 opened May 20, 2024 by suncimu
Issue with rerunning orthofinder "from trees" step -- Blast0_0.txt not found
#899 opened May 10, 2024 by 00-kelvin
Which directories for versions of Orthofinder v2.4.0 (or more recent) are valid with the HOGs?
#898 opened May 10, 2024 by SheepwormJM
Inferring gene trees with for orthogroups with less than 4 sequences
#897 opened May 9, 2024 by niconps14
1
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
Rooted species tree branch length meaning
#885 opened Mar 8, 2024 by jmpolinski
1
ERROR when starting from BLAST, Orthogroups or Tree
#884 opened Mar 4, 2024 by geboro
[Feature request] reduce number generated files per directory (e.g. for blast results, pickle files)
#883 opened Feb 22, 2024 by mpice-mn
[Bug:] Option -p tmp_pickle_dir not working
#882 opened Feb 21, 2024 by mpice-mn
conda install failes
#881 opened Feb 20, 2024 by shbrainard
1
Issue with user supplied species tree
#879 opened Feb 15, 2024 by mollylRivers
Installing on Mac M1 - README update
#878 opened Feb 14, 2024 by Neato-Nick
different sets of genes as input
#876 opened Feb 13, 2024 by NilsHassel
paralogs in same species
#875 opened Feb 13, 2024 by NilsHassel
-M msa -T raxml fails in OrthoFinder 2.5.5
#871 opened Dec 20, 2023 by wpfeiffer
Orthofinder not writing gene to HOG even though it matches all others in the group
#870 opened Dec 13, 2023 by A-Swafford
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