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@ -5,22 +5,22 @@ The core EukPhylo pipeline comprises two main components, which we refer to as E
We also provide a suite of utility scripts for describing data output by EukPhylo (e.g. basic sequence statistics such as composition, coverage, and length) as well as performing some of EukPhylo's more complex operations (e.g. "clade-grabbing") in a stand-alone form.
## EukPhylo Part 1 – Gene family assignment
* [Overview and modularity](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-1:-gf-assignment#overview-and-modularity)
* [Setup](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-1:-gf-assignment#setup)
* [The Hook Database](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-1:-gf-assignment#the-hook-database)
* [Running EukPhylo Part 1](https://github.com/Katzlab/EukPhylo/wiki/PhyloToL-Part-1:-gf-assignment#running-phylotol-part-1)
* [Processing transcriptomes](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-1:-gf-assignment#processing-transcriptomes)
* [Processing genomes](https://github.com/Katzlab/EukPhylo/wiki/Part1phylotol-part-1:-gf-assignment#processing-genomes)
* [Overview and modularity](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-part-1:-gf-assignment#overview-and-modularity)
* [Setup](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-part-1:-gf-assignment#setup)
* [The Hook Database](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-part-1:-gf-assignment#the-hook-database)
* [Running EukPhylo Part 1](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-Part-1:-gf-assignment#running-EukPhylo-part-1)
* [Processing transcriptomes](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-part-1:-gf-assignment#processing-transcriptomes)
* [Processing genomes](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-part-1:-gf-assignment#processing-genomes)
## EukPhylo Part 2 – MSAs, gene trees, and contamination loop
* [Overview and modularity](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#overview-and-modularity)
* [Setup](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#setup)
* [Databases](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#databases)
* [Running PhyloToL Part 2](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop)
* [Overlap and similarity filters](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#overlap-and-similarity-filters)
* [Guidance](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#guidance)
* [Gene trees](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#gene-trees)
* [Contamination loop: phylogeny-informed contamination removal](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#contamination-loop)
* [Overview and modularity](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-part-2:-MSAs,-trees,-and-contamination-loop#overview-and-modularity)
* [Setup](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-part-2:-MSAs,-trees,-and-contamination-loop#setup)
* [Databases](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-part-2:-MSAs,-trees,-and-contamination-loop#databases)
* [Running EukPhylo Part 2](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-part-2:-MSAs,-trees,-and-contamination-loop)
* [Overlap and similarity filters](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-part-2:-MSAs,-trees,-and-contamination-loop#overlap-and-similarity-filters)
* [Guidance](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-part-2:-MSAs,-trees,-and-contamination-loop#guidance)
* [Gene trees](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-part-2:-MSAs,-trees,-and-contamination-loop#gene-trees)
* [Contamination loop: phylogeny-informed contamination removal](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-part-2:-MSAs,-trees,-and-contamination-loop#contamination-loop)
## Other
* [Utility scripts](https://github.com/Katzlab/EukPhylo/wiki/Utilities)