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Katzlab 2024-08-09 17:18:36 -04:00
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@ -12,11 +12,11 @@ We also provide a suite of utility scripts for describing data output by PhyloTo
* [Processing genomes](https://github.com/Katzlab/PhyloToL-6/wiki/Part1phylotol-part-1#processing-genomes) * [Processing genomes](https://github.com/Katzlab/PhyloToL-6/wiki/Part1phylotol-part-1#processing-genomes)
## PhyloToL Part 2 ## PhyloToL Part 2
* [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/Part2) * [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#overview-and-modularity)
* [Overlap and similarity filters](https://github.com/Katzlab/PhyloToL-6/wiki/Part2) * [Overlap and similarity filters](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#overlap-and-similarity-filters)
* [Guidance](https://github.com/Katzlab/PhyloToL-6/wiki/Part2) * [Guidance](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#guidance)
* [Building gene trees](https://github.com/Katzlab/PhyloToL-6/wiki/Part2) * [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/Part2) * [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)