MiqoGraph: Fitting admixture graphs using mixed-integer quadratic optimization

• Main Authors: Narasimhan, V.M (Author), Patterson, N. (Author), Yan, J. (Author)
• Format: Article
• Language: English
• Published: Oxford University Press 2021
• Subjects: article; bioinformatics; simulation; velocity
• Online Access: View Fulltext in Publisher
• ISBN: 13674803 (ISSN)
• DOI: 10.1093/bioinformatics/btaa988

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. © C The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: [e-mail].