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+# Overview:
+PhyloToL is… 
+
+# Table of Contents
+
+
+## Introduction
+
+## PhyloToL Part I = determining gene families
+### Overview
+### ## Set up
+### ## The hook - for determining gene families
+### ## Processing transcriptomes
+### ## Processing genomes with CDs
+### ## Starting at different points in the process (Folder structure)
+### ## Appendices
+
+##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 
+### Contamination loop - additional curation 
+
+## Databases
+### PTL6-Hook
+### 1000 taxa ready to go’s
+### 1000 taxa curated for 500 GFs
+
+## Utilities
+
+## Troubleshooting Guide
+
+## Appendices