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

Auden Cote-L'Heureux 2025-01-10 10:59:50 -05:00
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PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md

@ -131,7 +131,7 @@ After homology assessment and building MSAs (the Guidance step), PhyloToL trims
Argument | Default | Choices | Description Argument | Default | Choices | Description
-- | -- | -- | -- -- | -- | -- | --
--tree_method | iqtree | iqtree, raxml, all | Program to use for tree-building. --tree_method | iqtree | iqtree, raxml, fasttree | Program to use for tree-building.
## Contamination loop ## Contamination loop