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

Godwin N. Ani 2025-07-17 14:51:37 -04:00
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EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md

@ -135,7 +135,7 @@ Argument | Default | Choices | Description
## Gene trees ## Gene trees
After homology assessment and building MSAs (the Guidance step), EukPhylo trims alignments and build trees. By default, alignments are trimmed at 0.95% with TrimAL, and trees by default are built by IqTREE with an LG+G model; users may choose to use a different third-party tool for phylogenetic reconstruction. After homology assessment and building MSAs (the Guidance step), EukPhylo trims alignments and build trees. By default, columns in the alignments are trimmed at 70% gaps with TrimAL, and trees by default are built by IqTREE with an LG+G model; users may choose to use a different third-party tool for phylogenetic reconstruction.
Argument | Default | Choices | Description Argument | Default | Choices | Description
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