miqoGraph: fitting admixture graphs using mixed-integer quadratic optimization

Abstract

Summary: Admixture graphs represent the genetic relationship between a set of populations through splits, drift and admixture. In this article, we present the Julia package miqoGraph, which uses mixed-integer quadratic optimization to fit topology, drift lengths and admixture proportions simultaneously. Through applications of miqoGraph to both simulated and real data, we show that integer optimization can greatly speed up and automate what is usually an arduous manual process.

Availability and implementation: https://github.com/juliayyan/PhylogeneticTrees.jl.

Supplementary information: Supplementary data are available at Bioinformatics online.