diff --git a/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md b/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md
index 78c1d62..364deca 100644
--- a/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md
+++ b/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md
@@ -11,7 +11,7 @@ For those users interested in eukaryotic phylogeny, we provide a database of 1,0
 
 # Running PhyloToL Part 2
 
-Running PhyloToL Part 2 requires at least 4 items in your main directory: 1) A folder named Scripts and containing all scripts from PhyloToL part 2 (**TBD - link to Github?), 2) a folder containing your input files, 3) a taxon list (**TBD - provide example below?) and 4) an OG list (**TBD - provide example below?). Given that PhyloToL part 2 is highly modular and flexible, you will want to be sure of what point to the process of PTLp2 you wish to start and end (**TBD - point to figshare file here -- some figure). The default script starts with raw data and produces trees using scripts 1 - TBD. 
+Running PhyloToL Part 2 requires at least 4 items in your main directory: 1) A folder named [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL2/Scripts) and containing all scripts from PhyloToL part 2 (**TBD - link to Github?), 2) a folder containing your input files, 3) a taxon list (**TBD - provide example below?) and 4) an OG list (**TBD - provide example below?). Given that PhyloToL part 2 is highly modular and flexible, you will want to be sure of what point to the process of PTLp2 you wish to start and end (**TBD - point to figshare file here -- some figure). The default script starts with raw data and produces trees using scripts 1 - TBD. 
 
 The code to run PhyloToL Part 2 in full is
 > python Scripts/phylotol.py --start raw --end trees --gf_list  listofOGs.txt --taxon_list taxon_list.txt --data Input_folder --output Output_folder  > Output1.out