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

MCLeleu 2025-04-16 10:36:37 +02:00
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EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md

@ -132,6 +132,11 @@ Argument | Default | Choices | Description
--keep_temp | False | include or exclude the argument | Use this to keep ALL Guidance intermediate files.
--keep_iter / -z | False | include or exclude the argument  | Keep all Guidance iterations (beware this will be very large)
We initially developped EukPhylo using Guidance v2.0.2, and then updated the scripts with the newest version Guidance v1. Some changes might be necessary depending on the version of the tool the user downloaded:
* Using Guidance v2.0.2, the tool should be placed in the Script Folder of EukPhylo, and the corresponding run line uncommented from the contamination.py script
* Using Guidance v1, user should make sure to update the path to the tool in the corresponding run line and uncomment that line (in contamination.py script)
## 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.