Related Issues (20)
- "Invalid escape sequence" errors while starting OrthoFinder HOT 1
- Hello! I have 11 .faa files in a folder. I ran orthofinder -d -f /public/home/newfasta -t 64 -o output_orthofinder. But after 13-14 minutes process failed. There is no error. I opened slurm.out file then checked. there was written like below. HOT 1
- total identical sequences clustered into one orthogroup, but the topology of gene tree divided into multiple clades HOT 1
- Species tree make_ultrameric.py not working HOT 1
- [Possible Bug] The `-og` option doesn't stop after inferring orthogroups HOT 1
- [Feature Request] Allow for passing options to Diamond and other dependencies HOT 1
- Single copy orthologs (SCO) are not being generated HOT 1
- not an issue, clarification wanted for which sequences are represented in orthogroups HOT 4
- what is the Orthogroup column in N*.tsv? HOT 1
- Question_process_Orthofinder HOT 2
- issue with running Orthofinder HOT 2
- HIV teste 1 HOT 4
- About -a option: using pre-computed BLAST results does not increase the number of orthofinder threads HOT 1
- Option to start Orthofinder at stage of inferring trees from MSAs? HOT 1
- header changed in MSA
- Diamond stuck on "Running diamond all-versus-all" HOT 1
- Option to stop Orthofinder after building the species tree? HOT 2
- Running OrthoFinder with Large Species Set (>2k) and Skipping GeneTree Construction HOT 2
- disagreement between OrthologuesStats_one-to-one.tsv and Orthogroups.GeneCount.tsv HOT 5
- Inferring remaining multiple sequence alignments and gene trees——This step has been stuck for ten days HOT 3
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from orthofinder.