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@@ -12,14 +12,13 @@ PhyloToL is…
 * The hook - for determining gene families
 * [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 (Folder structure)
-* Appendices
+* [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 
+* [Making Trees](https://docs.google.com/document/d/1pXMPZwK17yfk5-kIGYzwTSTO-5ggoMq-5II16nAPWAo/edit#heading=h.5f0xducehljc) 
 * Contamination loop - additional curation 
 
 ## Databases