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Katzlab 2024-08-12 10:17:57 -04:00
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@ -6,11 +6,11 @@ We also provide a suite of utility scripts for describing data output by PhyloTo
## PhyloToL Part 1 – Gene family assignment
* [Overview & 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#setup)
* [The Hook Database](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-1#the-hook-database)
* [Running PhyloToL Part 1](https://github.com/Katzlab/PhyloToL-6/wiki/PhyloToL-Part-1#running-phylotol-part-1)
* [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)
* [Setup](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-1:-gf-assignment#setup)
* [The Hook Database](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-1:-gf-assignment#the-hook-database)
* [Running PhyloToL Part 1](https://github.com/Katzlab/PhyloToL-6/wiki/PhyloToL-Part-1:-gf-assignment#running-phylotol-part-1)
* [Processing transcriptomes](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-1:-gf-assignment#processing-transcriptomes)
* [Processing genomes](https://github.com/Katzlab/PhyloToL-6/wiki/Part1phylotol-part-1:-gf-assignment#processing-genomes)
## PhyloToL Part 2 – MSAs, gene trees, species trees
* [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#overview-and-modularity)