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Katzlab 2024-08-10 15:45:55 -04:00
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@ -4,7 +4,7 @@ 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 – Gene family assignment
* [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-1#overview-and-modularity) * [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-1#overview-and-modularity)
* [Setup](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-1#setup) * [Setup](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-1#setup)
* [The Hook Database](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-1#the-hook-database) * [The Hook Database](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-1#the-hook-database)
@ -12,7 +12,7 @@ We also provide a suite of utility scripts for describing data output by PhyloTo
* [Processing transcriptomes](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-1#processing-transcriptomes) * [Processing transcriptomes](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-1#processing-transcriptomes)
* [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 – MSAs, gene trees, species trees
* [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#overview-and-modularity) * [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#overview-and-modularity)
* [Setup](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#setup) * [Setup](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#setup)
* [Databases] * [Databases]