Strong Selection Pressure Significantly Increases Epistatic Interactions in the Long-Term Evolution of a Protein
Aditi Gupta and Christoph Adami

Meta data describing the data deposited in Dryad. For any questions, email to agupta@msu.edu.

1. protease_sequences_1998_to_2006.zip
This folder contains:
	'*.consensus_added': multiple sequence alignment (MSA) of protease sequences from each year (1998-2006).
	'*.consensus_added_dict_pos.txt': counts for residues at each position in the MSA (output of getDictCounts_allpos.py)
	'*.consensus_added_dict_pos.txt_NSB_hpos.txt': per-site entropies calulated by NSB method (using script run_nsb.m)
	'*.consensus_added_dict_pos.txt_NSB_hpair.txt': pairwise entropies calculated using run_nsb.m
	'*.consensus_added_dict_pos.txt_NSB_mi.txt': mutual information calculated using run_nsb.m

2. longitudinal_protease_sequences.zip
This folder contains sequence files from longitudinal study. File descriptions are same as in protease_sequences_1998_to_2006.zip.

3. scripts.zip
This folder contains:
	generate_subsamples.py: script to read sequence file and resample (without replacement) N datasets with M sequences each.
	getDictCounts_allpos.py: reads MSA file and generates counts for residues at each position in MSA, as well as counts for residues at each pair of positions.
	run_nsb.m: Matlab code to compute entropies and mutual information using the NSB method. Need to install NSB first to use this.

4. Figure_generator.ipynb
This is an ipython notebook that reads the data files and generates figures.

June 9th, 2015.