Updated PhyloToL Part 2: MSAs, trees, and contamination loop (markdown)

PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md

@@ -32,6 +32,8 @@ For those users interested in eukaryotic phylogeny, we provide a database of 1,0
 
 # Running PhyloToL Part 2
 
+You can find exemplar Run for PhyloToL in [figshare](https://figshare.com/account/projects/196552/articles/26662018?file=48495760)
+
 Once you have set up your run folder as described in the Setup section above, you're ready to run PhyloToL part 2. The pipeline is highly modular, and contains five main sections:
 1. pre-Guidance (groups your sequences by GF instead of by sample and applies some basic filters; produces an unaligned amino acid file for each GF)
 2. Guidance (aligns your amino acid sequences and iteratively removes putative non-homologs; produces an aligned amino acid file for each GF)
@@ -140,6 +142,8 @@ The CL runs iteratively and users must set the number of times that rules should
 
 ### Contamination loop setup
 
+You can find exemplar Run for the Contamination Loop in [figshare](https://figshare.com/account/projects/196552/articles/26662018?file=48495760)
+
 The CL requires 1) a folder of alignments (it is most correct to not give gap trimmed alignments here) and 2) a folder of gene trees, and they should be formatted in the same way as output by the preceding steps of PhyloToL part 2 (i.e. in the "Output" folder, see above); most importantly, the alignment and tree files should begin with the same unique GF identifer. You can also give it data _not_ output by PhyloToL, but you will need to match the folder, file, and sequence name formats.
 
 You will also need to create a 'rules' file to define which sequences should be removed in which circumstances. The format here varies between the different modes of the CL, but they are all tab-separated files. Examples can be found in [Datasets S8-S12 on this project's Figshare](https://doi.org/10.6084/m9.figshare.26540599).