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Auden Cote-L'Heureux 2025-01-10 11:14:41 -05:00
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@ -4,8 +4,6 @@ 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.
Example output files for PhyloToL part 2 and the contamination loop can be found [here](https://doi.org/10.6084/m9.figshare.26662018.v1).
## PhyloToL Part 1 – Gene family assignment
* [Overview and modularity](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-1:-gf-assignment#overview-and-modularity)
* [Setup](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-1:-gf-assignment#setup)