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rebeccagawron 2024-01-23 12:13:56 -05:00
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@ -12,14 +12,13 @@ PhyloToL is…
* The hook - for determining gene families * The hook - for determining gene families
* [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 (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)
* Appendices
## 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 MSA - curated or not (PreG - Guidance)
* Filtering on GC3 content * Filtering on GC3 content
* Making Trees * [Making Trees](https://docs.google.com/document/d/1pXMPZwK17yfk5-kIGYzwTSTO-5ggoMq-5II16nAPWAo/edit#heading=h.5f0xducehljc)
* Contamination loop - additional curation * Contamination loop - additional curation
## Databases ## Databases