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Katzlab 2024-08-12 10:23:02 -04:00
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@ -12,7 +12,7 @@ We also provide a suite of utility scripts for describing data output by PhyloTo
* [Processing transcriptomes](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-1:-gf-assignment#processing-transcriptomes)
* [Processing genomes](https://github.com/Katzlab/PhyloToL-6/wiki/Part1phylotol-part-1:-gf-assignment#processing-genomes)
## PhyloToL Part 2 – MSAs, gene trees, species trees
## PhyloToL Part 2 – MSAs, gene trees, and contamination loop
* [Overview and modularity](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#overview-and-modularity)
* [Setup](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#setup)
* [Databases](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#databases)