(1) Unzip LANL Dataset HIVDB-2017-DNA.tgz
.... (1a) We will use data from folder: HIV1-2017-Filtered
.... (1b) Avoid the file "FLTHIV1COMPLETE2017DNA.fasta" as we want to use data separated by gene.
(2) Git clone hyphy (https://github.com/veg/hyphy) and install.
(3) Git clone hyphy-standalone-analyses (https://github.com/veg/hyphy-analyses)
(4) Data cleanup.. Codon aware MSA (https://github.com/veg/hyphy-analyses/tree/master/codon-msa)
.... (4a) For Protein MSA, used MAFFT (https://mafft.cbrc.jp/alignment/software/).
(5) Seaview, for NJ Tree (http://doua.prabi.fr/software/seaview)
(6) Run FUBAR
(7) Run FEL
(8) Exploratory Data Analysis (EDA) on LANL data.
(9) HyPhy Vision (http://vision.hyphy.org/) to see the .json files
(10) ???

1. HyPhy; "HyPhy: hypothesis testing using phylogenies", https://www.ncbi.nlm.nih.gov/pubmed/15509596
   
2. FUBAR; "FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection", https://academic.oup.com/mbe/article/30/5/1196/998247
   
3. MEME; "Detecting Individual Sites Subject to Episodic Diversifying Selection", https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002764
   
4. FEL; "Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection" https://academic.oup.com/mbe/article/22/5/1208/1066893
   

1. https://www.datamonkey.org/
   
2. http://hyphy.org/