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Katzlab 2024-08-12 10:20:09 -04:00
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@ -16,7 +16,7 @@ We also provide a suite of utility scripts for describing data output by PhyloTo
* [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)
* [Running PhyloToL Part 2]
* [Running PhyloToL Part 2](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop)
* [Overlap and similarity filters](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#overlap-and-similarity-filters)
* [Guidance](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#guidance)
* [Gene trees](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#gene-trees)