PottsEvolver

Documentation for PottsEvolver. In construction.

using Pkg
Pkg.add("PottsEvolver")
using PottsEvolver

Simulate evolution of protein sequences (or other) using a Potts model.

• Discrete or continuous time sampling.
• Sample single MCMC chains, or along branches of a tree.
• Sampling can take the genetic code into account.

Note: the package relies on two personal packages

• TreeTools.jl to handle phylogenetic trees
• BioSequenceMappings.jl to handle sequence alignments and to convert amino acids to digits.

Remaining issues:

• sampling not reproducible when picking a random seed.
• use of Alphabet not clear: it's part of the PottsGraph, but only the default alphabets can really be used.