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291 Open 638 Closed
291 Open 638 Closed
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Issues list

--assign seems to be broken in v3.0.1b1
#961 opened Jan 10, 2025 by macmanes
Renamed protein names in final orthogroup table
#960 opened Jan 9, 2025 by nat2bee
Inferring deep orthology or how to use "groups" instead of species
#959 opened Jan 8, 2025 by RekValT
1
Are othrogroups created by OrthoFinder mutually exclusive and exhaustive? How are isoforms of a gene handled?
#958 opened Jan 7, 2025 by soumitrakp
2
Using OrthoFinder, input the fa protein file downloaded from NCBI and obtain species tree. Is this species tree very correct?
#956 opened Dec 27, 2024 by helloworldABCD1234
1
Adding more species takes less time - unclear why?
#955 opened Dec 23, 2024 by 000generic
4
How to find genes in species-specific orthogroups from the output files?
#954 opened Dec 23, 2024 by Tang-WG
1
mcl added garbage entries
#953 opened Dec 17, 2024 by jarrTecn
1
RuntimeError: maximum recursion depth exceeded
#952 opened Dec 15, 2024 by oddguyeee
1
MSA error with version v3.0.1b1
#951 opened Dec 12, 2024 by macmanes
1
MSA workflow takes so much time. any other ways to get a accurate species tree?
#950 opened Dec 9, 2024 by Samadhi9
3
No Support Values
#949 opened Dec 9, 2024 by TT1972
1
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
ProTip! Add no:assignee to see everything that’s not assigned.