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Updated PhyloToL Part 2 (markdown)

Katzlab 2024-08-10 15:53:47 -04:00
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PhyloToL-Part-2.md → PhyloToL-Part-2-‐-MSAs,-CL,-Trees.md

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# Overview and Modularity
PhyloToL Part 2 is designed to: 1) generate multisequence alignments (**MSAs**) using Guidance (ref/github link ******), iterating to remove sequences that are not homologous (default sequence score is ****); 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 (see BioRxiv); and 4) ortholog selection and generation of species trees from concatenated alignments.
# Set Up
Requirements include: fasta files with controlled names.
# Databases