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@@ -8,12 +8,12 @@ PhyloToL is…
 
 ## 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
+###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