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Katzlab 2024-01-04 14:00:25 -05:00
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@ -7,25 +7,25 @@ PhyloToL is…
## Introduction ## Introduction
## PhyloToL Part I = determining gene families ## PhyloToL Part I = determining gene families
### Overview Overview
###Set up Set up
###The hook - for determining gene families The hook - for determining gene families
###Processing transcriptomes Processing transcriptomes
###Processing genomes with CDs Processing genomes with CDs
###Starting at different points in the process (Folder structure) Starting at different points in the process (Folder structure)
###Appendices 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
### Contamination loop - additional curation Contamination loop - additional curation
## Databases ## Databases
### PTL6-Hook PTL6-Hook
### 1000 taxa ready to go’s 1000 taxa ready to go’s
### 1000 taxa curated for 500 GFs 1000 taxa curated for 500 GFs
## Utilities ## Utilities