From b41890f02fc96be9570650383d61d16a2f8ba085 Mon Sep 17 00:00:00 2001 From: Katzlab Date: Fri, 9 Aug 2024 10:35:39 -0400 Subject: [PATCH] Updated Home (markdown) --- Home.md | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/Home.md b/Home.md index 0cf4c3b..a8714d8 100644 --- a/Home.md +++ b/Home.md @@ -9,22 +9,17 @@ PhyloToL is… ## PhyloToL Part I = determining gene families * Overview * [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 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) ## PhyloToL Part 2 = generating MSAs and gene trees * Overview of the process -* Producing MSA - curated or not (PreG - Guidance) -* Filtering on GC3 content -* [Making Trees](https://docs.google.com/document/d/1pXMPZwK17yfk5-kIGYzwTSTO-5ggoMq-5II16nAPWAo/edit#heading=h.5f0xducehljc) -* Contamination loop - additional curation - -## Databases -PTL6-Hook -1000 taxa ready to go’s -1000 taxa curated for 500 GFs +* Producing and curating MSAs +* Filtering by composition +* [Building gene trees](https://docs.google.com/document/d/1pXMPZwK17yfk5-kIGYzwTSTO-5ggoMq-5II16nAPWAo/edit#heading=h.5f0xducehljc) +* Contamination loop: phylogeny-informed contamination removal ## Utilities