OutOfEquilibrium-ProtSeq

Getting started

Clone this repository on your local machine by running

git clone git@github.com:Bitbol-Lab/OutOfEquilibrium-ProtSeq.git

and move inside the root folder.

2 states

The 2states folder contains three scripts to generate sequences. First, Generate_sequences_eq_cluster.py allows to generate independent sequences at equilibrium. Second, Generate_sequences_VaryingTemperature.py allows to generate sequences with varying selection strength (temperature). Note that an equilibrium dataset is needed to generate sequences with varying temperature because an equilibrium sequence is taken at the beginning of the evolution. Finally, Generate_sequences_phylogeny_binaryvariables.py allows to generate sequences with phylogeny using a random (non-functional) ancestor at the root of the phylogeny.

The code in Analyse_data.py allows to infer contacts using mean-field DCA.

Realistic model