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@@ -12,11 +12,11 @@ We also provide a suite of utility scripts for describing data output by PhyloTo
 * [Processing genomes](https://github.com/Katzlab/PhyloToL-6/wiki/Part1phylotol-part-1#processing-genomes)
 
 ## PhyloToL Part 2
-* [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/Part2)
-* [Overlap and similarity filters](https://github.com/Katzlab/PhyloToL-6/wiki/Part2)
-* [Guidance](https://github.com/Katzlab/PhyloToL-6/wiki/Part2) 
-* [Building gene trees](https://github.com/Katzlab/PhyloToL-6/wiki/Part2)
-* [Contamination loop: phylogeny-informed contamination removal](https://github.com/Katzlab/PhyloToL-6/wiki/Part2)
+* [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2#overview-and-modularity)
+* [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)