miqoGraph：使用混合整数二次优化拟合混合图。
miqoGraph: fitting admixture graphs using mixed-integer quadratic optimization.
机构信息
Operations Research Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
出版信息
Bioinformatics. 2021 Aug 25;37(16):2488-2490. doi: 10.1093/bioinformatics/btaa988.
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.
摘要
混合图通过分裂、漂移和混合来表示一组群体之间的遗传关系。本文介绍了一个名为 miqoGraph 的 Julia 包，它使用混合整数二次优化来同时拟合拓扑结构、漂移长度和混合比例。通过将 miqoGraph 应用于模拟和真实数据，我们表明整数优化可以大大加快和自动化通常非常繁琐的手动过程。
可用性和实现
https://github.com/juliayyan/PhylogeneticTrees.jl。
补充信息
补充数据可在Bioinformatics 在线获得。
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