Primary Release

This has the main functionality of mfDCA: producing couplings, localfields, and DI pairs. It also has settings for reweighting strength, custom dictionaries for the sequence symbols, memory management for the pairwise distance calculations to run in low memory settings, and has Hamiltonian scoring functionality for full-sequence and inter-domain pairings.

It has plotting functionality, mapping of alignments using HMMs, and other standard tools our group uses for routine analysis.

It has unit testing as well, and performance measures were not done systematically but it feels fast enough.

vae_dependency

Supports LGL-VAE. Not recommended for other uses.