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Katzlab 2024-08-10 04:46:02 -04:00
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@ -15,10 +15,12 @@ We also provide a suite of utility scripts for describing data output by PhyloTo
## PhyloToL Part 2 ## PhyloToL Part 2
* [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#overview-and-modularity) * [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#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#setup)
* [Overlap and similarity filters](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#overlap-and-similarity-filters) * [Databases]
* [Guidance](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#guidance) * [Running PhyloToL Part 2]
* [Gene trees](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#gene-trees) * [Overlap and similarity filters](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#overlap-and-similarity-filters)
* [Contamination loop: phylogeny-informed contamination removal](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#contamination-loop) * [Guidance](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#guidance)
* [Gene trees](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#gene-trees)
* [Contamination loop: phylogeny-informed contamination removal](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#contamination-loop)
## Other ## Other
* [Utility scripts](https://github.com/Katzlab/PhyloToL-6/wiki/Utilities) * [Utility scripts](https://github.com/Katzlab/PhyloToL-6/wiki/Utilities)