Issues

• IQTREE with BLAST for 50+ proteomes

  davidemms/OrthoFinder#1035 · Filter by author mrizwan-riaz opened on Sep 11, 2026

• IQTREE3 error

  davidemms/OrthoFinder#1033 · Filter by author katieemelianova opened on Jul 6, 2026
  1

• How to determine an optimal MCL inflation value when no ground-truth orthogroups are available?

  davidemms/OrthoFinder#1032 · Filter by author sasupty opened on Jun 3, 2026
  1

• SCO count with DIAMOND and DIAMOND_ULTRA_SENS in OrthoFinder — interpretation and MCL inflation advice?

  davidemms/OrthoFinder#1031 · Filter by author sasupty opened on May 21, 2026
  1

• Discrepancy between BUSCO single-copy genes and OrthoFinder single-copy orthogroups in fungal comparative genomics

  davidemms/OrthoFinder#1030 · Filter by author sasupty opened on May 18, 2026
  2

• [Errno 2] No such file or directory Multisequence Alignments

  davidemms/OrthoFinder#1029 · Filter by author anearman opened on May 16, 2026
  4

• the early version of orthofinder returns errors

  davidemms/OrthoFinder#1028 · Filter by author KVin1456 opened on Apr 15, 2026
  1

• ERROR in parallel process - after finish commands of genetrees and -fgt

  davidemms/OrthoFinder#1027 · Filter by author david6git opened on Apr 10, 2026
  3

• Mismatch between Orthogroups.tsv and WorkingDirectory/Trees_ids/*.txt for a small number of OGs by OrthoFinder v3.1.3

  davidemms/OrthoFinder#1026 · Filter by author BioOmics opened on Apr 10, 2026
  2

• Question about missing Gene_Trees output in OrthoFinder v3.1.1 for downstream ASTRAL analysis

  davidemms/OrthoFinder#1025 · Filter by author shuyuanao opened on Apr 6, 2026
  1

• ERROR: Stalled for 200.0s

  davidemms/OrthoFinder#1024 · Filter by author lfaino opened on Apr 3, 2026
  8

• BLAST results not showing

  davidemms/OrthoFinder#1023 · Filter by author QGirasek opened on Mar 11, 2026
  3

• Error code: -9

  davidemms/OrthoFinder#1021 · Filter by author BWY9394 opened on Jan 20, 2026
  2

• Phylogenetic_Hierarchical_Orthogroups and Nx.tsv

  davidemms/OrthoFinder#1020 · Filter by author pfb2201 opened on Jan 8, 2026
  4

• OrthoFinder run does not produce N0.tsv file

  davidemms/OrthoFinder#1019 · Filter by author alexweisberg opened on Jan 8, 2026
  2

• Missing orthogroup .fa input files to famsa

  davidemms/OrthoFinder#1017 · Filter by author serenalotreck opened on Dec 2, 2025
  14

• Can i use orthofinder for a SUBSET of proteins?

  davidemms/OrthoFinder#1016 · Filter by author Alexkortsi opened on Nov 25, 2025
  1

• Consultation on OrthoFinder Batch Processing Strategy for 239 Species

  davidemms/OrthoFinder#1015 · Filter by author alex-per opened on Nov 7, 2025
  1

• Diamond sporious error. I need to use the flag --ignore-warnings

  davidemms/OrthoFinder#1012 · Filter by author jarrTecn opened on Oct 28, 2025
  2

• Not producing MSAs and gene trees

  davidemms/OrthoFinder#1011 · Filter by author smfrazee opened on Oct 12, 2025
  3

• Unexpectedly high number of unassigned genes in reference genome

  davidemms/OrthoFinder#1010 · Filter by author jiaowu123 opened on Sep 11, 2025
  4

• How to correctly resume orthofinder after manually running mcl?

  davidemms/OrthoFinder#1009 · Filter by author ayyyy-c opened on Sep 5, 2025
  3

• Unclear Error During Very Large-Scale Orthogroup Inference with OrthoFinder 3

  davidemms/OrthoFinder#1008 · Filter by author liweisdau1991 opened on Sep 3, 2025
  2

• One gene copy in polyploid species excluded from orthogroup despite high similarity

  davidemms/OrthoFinder#1007 · Filter by author smirsyad22 opened on Sep 1, 2025
  3

• msa

  davidemms/OrthoFinder#1006 · Filter by author aebaci opened on Aug 22, 2025
  1