miqoGraph: fitting admixture graphs using mixed-integer quadratic optimization | Zendy

Julia Yan | Zendy; Nick Patterson | Zendy; Vagheesh M. Narasimhan | Zendy

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miqoGraph: fitting admixture graphs using mixed-integer quadratic optimization

Author(s) -

Julia Yan,

Nick Patterson,

Vagheesh M. Narasimhan

Publication year - 2020

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btaa988

Subject(s) - integer (computer science) , quadratic equation , set (abstract data type) , computer science , process (computing) , r package , algorithm , quadratic programming , genetic algorithm , software package , data set , integer programming , mathematical optimization , software , theoretical computer science , mathematics , artificial intelligence , machine learning , computational science , programming language , geometry

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.

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