diff --git a/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md b/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md index c677856..153b7e5 100644 --- a/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md +++ b/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. Core parameters - rarely changed from defaults + +Argument | Default | Choices | Help +-- | -- | -- | -- --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. --similarity_filter | store_true |   | Run the similarity filter in pre-Guidance.