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@@ -15,10 +15,12 @@ We also provide a suite of utility scripts for describing data output by PhyloTo
 ## PhyloToL Part 2
 * [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#overview-and-modularity)
 * [Setup](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#setup)
-* [Overlap and similarity filters](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#overlap-and-similarity-filters)
-* [Guidance](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#guidance) 
-* [Gene trees](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#gene-trees)
-* [Contamination loop: phylogeny-informed contamination removal](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#contamination-loop)
+* [Databases]
+* [Running PhyloToL Part 2]
+  * [Overlap and similarity filters](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#overlap-and-similarity-filters)
+  * [Guidance](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#guidance) 
+  * [Gene trees](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#gene-trees)
+  * [Contamination loop: phylogeny-informed contamination removal](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#contamination-loop)
 
 ## Other
 * [Utility scripts](https://github.com/Katzlab/PhyloToL-6/wiki/Utilities)