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@@ -5,18 +5,18 @@ The core PhyloToL pipeline comprises two main components, which we refer to as P
 We also provide a suite of utility scripts for describing data output by PhyloToL (e.g. basic sequence statistics such as composition, coverage, and length) as well as performing some of PhyloToL's more complex operations (e.g. "clade-grabbing") in a stand-alone form.
 
 ## PhyloToL Part 1
-* [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/PTL1-Overview)
-* [Set up](https://github.com/Katzlab/PhyloToL-6/wiki/Set-up)
-* [The Hook Database](https://github.com/Katzlab/PhyloToL-6/wiki/Hook)
-* [Processing transcriptomes](https://github.com/Katzlab/PhyloToL-6/wiki/Processing-transcriptomes)
-* [Processing genomes](https://github.com/Katzlab/PhyloToL-6/wiki/Processing-genomes)
+* [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/Part1)
+* [Set up](https://github.com/Katzlab/PhyloToL-6/wiki/Part1)
+* [The Hook Database](https://github.com/Katzlab/PhyloToL-6/wiki/Part1)
+* [Processing transcriptomes](https://github.com/Katzlab/PhyloToL-6/wiki/Part1)
+* [Processing genomes](https://github.com/Katzlab/PhyloToL-6/wiki/Part1)
 
 ## PhyloToL Part 2
-* [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/PTL2-Overview)
-* [Overlap and similarity filters](https://github.com/Katzlab/PhyloToL-6/wiki/pre-Guidance)
-* [Guidance](https://github.com/Katzlab/PhyloToL-6/wiki/Guidance) 
-* [Building gene trees](https://github.com/Katzlab/PhyloToL-6/wiki/Trees)
-* [Contamination loop: phylogeny-informed contamination removal](https://github.com/Katzlab/PhyloToL-6/wiki/Contamination-loop)
+* [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)
 
 ## Other
 * [Utility scripts](https://github.com/Katzlab/PhyloToL-6/wiki/Utilities)