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Updated PhyloToL Part 2: MSAs, trees, and contamination loop (markdown)

MCLeleu 2024-08-13 10:09:54 -04:00
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PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md

@ -115,6 +115,9 @@ Argument | Default | Choices | Help
--sim_taxa | None |   | Path to the file with the taxa (10-digit codes) to apply the similarity filter on. --sim_taxa | None |   | Path to the file with the taxa (10-digit codes) to apply the similarity filter on.
Core parameters - rarely changed from defaults Core parameters - rarely changed from defaults
Argument | Default | Choices | Help
-- | -- | -- | --
--blast_cutoff | 1e-20 |   | Blast e-value cutoff. --blast_cutoff | 1e-20 |   | Blast e-value cutoff.
--len_cutoff | 10 |   | Amino acid length cutoff for removal of very short sequences after column removal in Guidance. --len_cutoff | 10 |   | Amino acid length cutoff for removal of very short sequences after column removal in Guidance.
--similarity_filter | store_true |   | Run the similarity filter in pre-Guidance. --similarity_filter | store_true |   | Run the similarity filter in pre-Guidance.