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281 Open 637 Closed
281 Open 637 Closed
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Issues list

MSA workflow takes so much time. any other ways to get a accurate species tree?
#950 opened Dec 9, 2024 by Samadhi9
No Support Values
#949 opened Dec 9, 2024 by TT1972
ERROR: Species tree inference failed
#948 opened Dec 5, 2024 by dmckeow
1
error with 470 genomes
#947 opened Dec 2, 2024 by macmanes
1
UnassignedGenes——Species-SpecificGenes?
#946 opened Nov 29, 2024 by MegadogDede
4
Extract edge weights from graph file
#945 opened Nov 20, 2024 by gauravdiwan89
5
Are there HOG alignments and gene trees in OrthoFinder output?
#943 opened Nov 18, 2024 by 000generic
2
More species with lower quality genomes finishes faster
#942 opened Nov 16, 2024 by 000generic
2
issues with results post "--assign", single gene in multiple Orthogroups
#941 opened Nov 14, 2024 by nhartwic
4
error mcl -9 no such file "clusters_OrthoFinder_I1.5.txt"
#940 opened Nov 14, 2024 by cpouchon
5
User-specified species tree with core/assign workflow
#939 opened Nov 13, 2024 by SalvadorGJ
3
ERROR: Query or hit sequence ID in BLAST results file missing or incorrectly formatted
#938 opened Nov 13, 2024 by jrdred
3
orthofinder3 "assign" option failed
#937 opened Nov 12, 2024 by uguyet
4
Sequence IDs in single copy orthologs from RefSeq cds data
#935 opened Nov 7, 2024 by marctollis
1
Importing Custom Rooted Gene Trees into OrthoFinder for DLC Analysis
#934 opened Nov 7, 2024 by Li-Yuanshuo
1
User-specified rooted species tree
#933 opened Nov 6, 2024 by dahaigui
1
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
12
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
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
ProTip! Add no:assignee to see everything that’s not assigned.