How to filter Hmmsearch alignment

Question

[Yongjie Zhang]

Dear All,

After performing hmmsearch, there is a line representing the posterior probability (PP) of each aligned residue in the alignment section. I'd like to keep only amino acids that were aligned with a PP value of 1.0 for phylogenetic analysis, but I'm not sure how to filter amino acids based on PP values from the Hmmsearch output. Please let me know if you have any suggestions.

Thanks,

Yongjie

[Mensur Dlakic]

I don't know how to help with your main question, as this is an unusual approach. You will probably have to write a custom script. Before you do that, I urge you to consider whether this approach is valid. Residues with certain hmmsearch-derived posterior probabilities may or may not be the best choice for phylogenetic analyses.

If your goal is to trim the alignments, there are established approaches that will preserve evolutionary information.

• https://bmcecolevol.biomedcentral.com/articles/10.1186/1471-2148-10-210
• https://research.pasteur.fr/en/software/bmge-block-mapping-and-gathering-with-entropy/