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Katzlab 2024-08-09 15:08:21 -04:00
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@ -5,18 +5,18 @@ The core PhyloToL pipeline comprises two main components, which we refer to as P
We also provide a suite of utility scripts for describing data output by PhyloToL (e.g. basic sequence statistics such as composition, coverage, and length) as well as performing some of PhyloToL's more complex operations (e.g. "clade-grabbing") in a stand-alone form. We also provide a suite of utility scripts for describing data output by PhyloToL (e.g. basic sequence statistics such as composition, coverage, and length) as well as performing some of PhyloToL's more complex operations (e.g. "clade-grabbing") in a stand-alone form.
## PhyloToL Part 1 ## PhyloToL Part 1
* [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/PTL1-Overview) * [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/Part1)
* [Set up](https://github.com/Katzlab/PhyloToL-6/wiki/Set-up) * [Set up](https://github.com/Katzlab/PhyloToL-6/wiki/Part1)
* [The Hook Database](https://github.com/Katzlab/PhyloToL-6/wiki/Hook) * [The Hook Database](https://github.com/Katzlab/PhyloToL-6/wiki/Part1)
* [Processing transcriptomes](https://github.com/Katzlab/PhyloToL-6/wiki/Processing-transcriptomes) * [Processing transcriptomes](https://github.com/Katzlab/PhyloToL-6/wiki/Part1)
* [Processing genomes](https://github.com/Katzlab/PhyloToL-6/wiki/Processing-genomes) * [Processing genomes](https://github.com/Katzlab/PhyloToL-6/wiki/Part1)
## PhyloToL Part 2 ## PhyloToL Part 2
* [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/PTL2-Overview) * [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/Part2)
* [Overlap and similarity filters](https://github.com/Katzlab/PhyloToL-6/wiki/pre-Guidance) * [Overlap and similarity filters](https://github.com/Katzlab/PhyloToL-6/wiki/Part2)
* [Guidance](https://github.com/Katzlab/PhyloToL-6/wiki/Guidance) * [Guidance](https://github.com/Katzlab/PhyloToL-6/wiki/Part2)
* [Building gene trees](https://github.com/Katzlab/PhyloToL-6/wiki/Trees) * [Building gene trees](https://github.com/Katzlab/PhyloToL-6/wiki/Part2)
* [Contamination loop: phylogeny-informed contamination removal](https://github.com/Katzlab/PhyloToL-6/wiki/Contamination-loop) * [Contamination loop: phylogeny-informed contamination removal](https://github.com/Katzlab/PhyloToL-6/wiki/Part2)
## Other ## Other
* [Utility scripts](https://github.com/Katzlab/PhyloToL-6/wiki/Utilities) * [Utility scripts](https://github.com/Katzlab/PhyloToL-6/wiki/Utilities)