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Katzlab 2024-08-09 10:35:39 -04:00
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@ -9,22 +9,17 @@ PhyloToL is…
## PhyloToL Part I = determining gene families ## PhyloToL Part I = determining gene families
* Overview * Overview
* [Set up](https://github.com/Katzlab/PhyloToL-6/wiki/Set-up) * [Set up](https://github.com/Katzlab/PhyloToL-6/wiki/Set-up)
* The hook - for determining gene families * The Hook reference database for gene family assigment
* [Processing transcriptomes](https://docs.google.com/document/d/1pXMPZwK17yfk5-kIGYzwTSTO-5ggoMq-5II16nAPWAo/edit#heading=h.masnnqe0fycn) * [Processing transcriptomes](https://docs.google.com/document/d/1pXMPZwK17yfk5-kIGYzwTSTO-5ggoMq-5II16nAPWAo/edit#heading=h.masnnqe0fycn)
* [Processing genomes](https://docs.google.com/document/d/1pXMPZwK17yfk5-kIGYzwTSTO-5ggoMq-5II16nAPWAo/edit#heading=h.15uyieg4qumy) with CDs * [Processing genomes](https://docs.google.com/document/d/1pXMPZwK17yfk5-kIGYzwTSTO-5ggoMq-5II16nAPWAo/edit#heading=h.15uyieg4qumy) with CDs
* [Starting at different points in the process](https://docs.google.com/document/d/1pXMPZwK17yfk5-kIGYzwTSTO-5ggoMq-5II16nAPWAo/edit#heading=h.sjrzmygryaj4) (Folder structure) * [Starting at different points in the process](https://docs.google.com/document/d/1pXMPZwK17yfk5-kIGYzwTSTO-5ggoMq-5II16nAPWAo/edit#heading=h.sjrzmygryaj4) (Folder structure)
## PhyloToL Part 2 = generating MSAs and gene trees ## PhyloToL Part 2 = generating MSAs and gene trees
* Overview of the process * Overview of the process
* Producing MSA - curated or not (PreG - Guidance) * Producing and curating MSAs
* Filtering on GC3 content * Filtering by composition
* [Making Trees](https://docs.google.com/document/d/1pXMPZwK17yfk5-kIGYzwTSTO-5ggoMq-5II16nAPWAo/edit#heading=h.5f0xducehljc) * [Building gene trees](https://docs.google.com/document/d/1pXMPZwK17yfk5-kIGYzwTSTO-5ggoMq-5II16nAPWAo/edit#heading=h.5f0xducehljc)
* Contamination loop - additional curation * Contamination loop: phylogeny-informed contamination removal
## Databases
PTL6-Hook
1000 taxa ready to go’s
1000 taxa curated for 500 GFs
## Utilities ## Utilities