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Katzlab 2024-08-12 10:19:48 -04:00
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@ -14,13 +14,13 @@ We also provide a suite of utility scripts for describing data output by PhyloTo
## PhyloToL Part 2 – MSAs, gene trees, species trees ## PhyloToL Part 2 – MSAs, gene trees, species trees
* [Overview and modularity](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#overview-and-modularity) * [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#setup) * [Setup](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#setup)
* [Databases] * [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]
* [Overlap and similarity filters](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#overlap-and-similarity-filters) * [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#guidance) * [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#gene-trees) * [Gene trees](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#gene-trees)
* [Contamination loop: phylogeny-informed contamination removal](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#contamination-loop) * [Contamination loop: phylogeny-informed contamination removal](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#contamination-loop)
## Other ## Other
* [Utility scripts](https://github.com/Katzlab/PhyloToL-6/wiki/Utilities) * [Utility scripts](https://github.com/Katzlab/PhyloToL-6/wiki/Utilities)