Improve descriptions in README

I realized that it was previously a bit hard to understand the directory structure, namely that things are divided up by which virus we were looking at, and then which analyses were performed. This structure was chosen because the types of analyses performed varied between the 3 viruses. I edited the README to make it easier to understand this structure, and better point to where relevant data and results would be.
blab · Aug 8, 2018 · 4d07b48 · 4d07b48
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@@ -30,6 +30,7 @@ François Rouet<sup>1</sup> Janin Nouhin<sup>1</sup>, Du-Ping Zheng<sup>2</sup>
 Rouet et al. 2017. Massive iatrogenic outbreak of human immunodeficiency virus type 1 in rural Cambodia, 2014-2015. Clin Infect Dis: cix1071. [doi.org/10.1093/cid/cix1071](https://doi.org/10.1093/cid/cix1071)
 
 ### Primary data and analysis
+Below are brief descriptions of the analyses we conducted for this project, with links out to the directories in this repo that are pertinent to each analysis. Within analysis-specific repos you'll find READMEs that give a more in-depth explanation of the analysis, and that display the figures that were generated.
 
 * [Sequences and collection date data combined](Scripts/Python_scripts/Make_Fasta_Infiles.ipynb)
 * [Maximum likelihood analysis of HIV-Env](HIV/max_likelihood/)