NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.
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speciesrax/generax fix for excluded gene families #46
SpeciesRax and GeneRax both use RAxML under the hood to optimize tree topologies. Whereas IQ-TREE and MAFFt can handle some rare amino acids (I know at least selenocysteine - U, but possible also pyrrolysine - O), RAxML can't. So, if these are present in MSAs, these gene families are excluded from generax/speciesrax analysis.
This change just goes in and removes these from staged files in the generax and speciesrax modules. Seems to fix the issue.
SpeciesRax and GeneRax both use RAxML under the hood to optimize tree topologies. Whereas IQ-TREE and MAFFt can handle some rare amino acids (I know at least selenocysteine - U, but possible also pyrrolysine - O), RAxML can't. So, if these are present in MSAs, these gene families are excluded from generax/speciesrax analysis.
This change just goes in and removes these from staged files in the generax and speciesrax modules. Seems to fix the issue.