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

Auden Cote-L'Heureux 2025-01-10 11:14:59 -05:00
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PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md

@ -7,6 +7,8 @@ PhyloToL Part 2 is designed to:
PhyloToL part 2 starts from the “ReadyToGo” files produced by part 1 (or any set of fasta files of sequences per-taxon with names that match PhyloToL 6 criteria) and generates multisequence alignments and trees. The pipeline is modular, and can be started, paused and resumed at multiple points. Output and input options of this part of the pipeline are flexible: users can input a folder of amino acid ReadyToGo files output by part 1, unaligned amino acid sequences per gene family (GF; in which case pre-Guidance filters are not run), aligned sequence files (one file per each GF, in which case Guidance does not run), or even trees if a user is running only the contamination loop. Details are provided bellow.
Example output files for PhyloToL part 2 and the contamination loop can be found [here](https://doi.org/10.6084/m9.figshare.26662018.v1).
# Set Up
## Dependencies