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Missing orthogroup <code>.fa</code> input files to famsa

Status: Open.

#1017 In davidemms/OrthoFinder;

· serenalotreck opened on Dec 2, 2025

Can i use orthofinder for a SUBSET of proteins?

Status: Open.

#1016 In davidemms/OrthoFinder;

· Alexkortsi opened on Nov 25, 2025

Consultation on OrthoFinder Batch Processing Strategy for 239 Species

Status: Open.

#1015 In davidemms/OrthoFinder;

· alex-per opened on Nov 7, 2025

Diamond sporious error. I need to use the flag <code>--ignore-warnings</code>

Status: Open.

#1012 In davidemms/OrthoFinder;

· jarrTecn opened on Oct 28, 2025

Not producing MSAs and gene trees

Status: Open.

#1011 In davidemms/OrthoFinder;

· smfrazee opened on Oct 12, 2025

Unexpectedly high number of unassigned genes in reference genome

Status: Open.

#1010 In davidemms/OrthoFinder;

· jiaowu123 opened on Sep 11, 2025

How to correctly resume orthofinder after manually running mcl?

Status: Open.

#1009 In davidemms/OrthoFinder;

· ayyyy-c opened on Sep 5, 2025

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

Status: Open.

#1008 In davidemms/OrthoFinder;

· liweisdau1991 opened on Sep 3, 2025

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

Status: Open.

#1007 In davidemms/OrthoFinder;

· smirsyad22 opened on Sep 1, 2025

msa

Status: Open.

#1006 In davidemms/OrthoFinder;

· aebaci opened on Aug 22, 2025

Issue running OrthoFinder with IQ-TREE3 – problematic MSAs

Status: Open.

#1005 In davidemms/OrthoFinder;

· PPrabhu1997 opened on Aug 17, 2025

Error when adding new species using -b parameter to reuse OrthoFinder BLAST results

Status: Open.

#1004 In davidemms/OrthoFinder;

· Huangxiaoqin666 opened on Aug 14, 2025