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PAML codeml fails with exit status 1

Hi all, I am running a Nextflow pipeline for selection analysis (dN/dS) using BioPython's Bio.Phylo.PAML.codeml. When running on highly conserved genes (fusA) with near-zero sequence diversity (some isolates are 100% identical), codeml crashes with exit code 1. My question: What is the standard practice in automated pipelines when dealing with zero-diversity genes?

paml dnds phylogenomics
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written by Md Hasibul • Md Hasibul

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