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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. 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 ## EukPhylo Part 1 – Gene family assignment
* [Overview and modularity](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-1:-gf-assignment#overview-and-modularity) * [Overview and modularity](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-part-1:-gf-assignment#overview-and-modularity)
* [Setup](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-1:-gf-assignment#setup) * [Setup](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-part-1:-gf-assignment#setup)
* [The Hook Database](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-1:-gf-assignment#the-hook-database) * [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/PhyloToL-Part-1:-gf-assignment#running-phylotol-part-1) * [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/phylotol-part-1:-gf-assignment#processing-transcriptomes) * [Processing transcriptomes](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-part-1:-gf-assignment#processing-transcriptomes)
* [Processing genomes](https://github.com/Katzlab/EukPhylo/wiki/Part1phylotol-part-1:-gf-assignment#processing-genomes) * [Processing genomes](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-part-1:-gf-assignment#processing-genomes)
## EukPhylo Part 2 – MSAs, gene trees, and contamination loop ## 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) * [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/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#setup) * [Setup](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-part-2:-MSAs,-trees,-and-contamination-loop#setup)
* [Databases](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#databases) * [Databases](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-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) * [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/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#overlap-and-similarity-filters) * [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/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#guidance) * [Guidance](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-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) * [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/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#contamination-loop) * [Contamination loop: phylogeny-informed contamination removal](https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-part-2:-MSAs,-trees,-and-contamination-loop#contamination-loop)
## Other ## Other
* [Utility scripts](https://github.com/Katzlab/EukPhylo/wiki/Utilities) * [Utility scripts](https://github.com/Katzlab/EukPhylo/wiki/Utilities)