IntegerLinearProgramming-Phylogenetics

A Integer Linear Programming approach for solving MCR, MCCP, FMPP(using concept of hypercubes) along with NMF technique to boost MCCP solution.

The Bio-informatics problems tackled through this project are,

1. MCR - Minimum Character Removal Problem
2. MCCP - Maximum Character Compatibility Problem
3. FMPP - Full Maximum Parsimony Problem

Published

Optimal Perfect Phylogeny Using ILP and Continuous Approximations

Run Locally

Prerequisites For,

1. Excel - Open Solver, documentation and download - Here
2. MATLAB and Python - Gurobi Optimizer, documentation and download - Here

Code

The MCR (ILP), MCCP(ILP), and MCCP (NMF) solutions code files in,

1. Excel example hard-coded - File
2. MATLAB - File
3. Python - File

The FMPP solution in MATLAB - File