Modeling and in vitro testing of the HIV-1 Nef fitness landscape

Barton JP^*, Rajkoomar E^*, Mann JK, Murakowski DK, Toyoda M, Mahiti M, Mwimanzi P, Ueno T, Chakraborty AK⁺, Ndung’u T⁺

^* Equal contributions
⁺ Correspondence to ndungu@ukzn.ac.za, arupc@mit.edu

Data

Data used in our analysis is contained in the /raw folder. Processed data is stored in the /input and /output folders.

Ising and Potts models

Ising and Potts models were inferred from the sequence alignments raw/nef-B-clipped.fasta and raw/nef-C-clipped.fasta using ACE. Correlations computed from the sequence alignments, which serve as input to ACE, and output from the ACE program are included in the /couplings folder. See the main ACE repository for more information on these files.

Analysis

All analysis performed for the paper is contained in the Jupyter notebook nef-analysis.ipynb. Figures produced here are stored in the /figures folder.