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

Katzlab 2024-08-13 19:00:06 -04:00
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PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md

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# Overview and Modularity
PhyloToL Part 2 is designed to:
1. Generate multisequence alignments (**MSAs**) firsts filtering in a "Pre-Guidance" step and then using [Guidance](https://taux.evolseq.net/guidance/source) version 2.02 , iterating to remove sequences considered non-homologs (based on sequence score is 0.3)
1. Generate multisequence alignments (**MSAs**) after first filtering in a "Pre-Guidance" step and then using [Guidance](https://taux.evolseq.net/guidance/source) version 2.02 , iterating to remove sequences considered non-homologs (based on sequence score is 0.3)
2. Generate gene trees using a 3rd party program (RaxML, IQTree, FastTree)
3. Remove contaminating sequences with the "Contamination Loop" (**CL**) and user-defined rules for both sister/subsister and clade grabbing options
4) Select orthologs and construct concatenated alignments for building species trees.