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 sim...
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| Veröffentlicht in: | Bioinformatics (Oxford, England) England), 2021-08, Vol.37 (16), p.2488-2490 |
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| container_title | Bioinformatics (Oxford, England) |
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| creator | Yan, Julia Patterson, Nick Narasimhan, Vagheesh M |
| description | 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. |
| doi_str_mv | 10.1093/bioinformatics/btaa988 |
| format | Article |
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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.</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btaa988</identifier><language>eng</language><publisher>Oxford: Oxford University Press</publisher><subject>Admixtures ; Availability ; Bioinformatics ; Drift ; Genetic relationship ; Graphs ; Mixed integer ; Phylogeny ; Population genetics ; Topology ; Topology optimization</subject><ispartof>Bioinformatics (Oxford, England), 2021-08, Vol.37 (16), p.2488-2490</ispartof><rights>The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2020</rights><rights>The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c406t-9d107d9234ef635ad4515f39aaf1eededb906b1206d3b0778a4d7d3a0a21285e3</citedby><cites>FETCH-LOGICAL-c406t-9d107d9234ef635ad4515f39aaf1eededb906b1206d3b0778a4d7d3a0a21285e3</cites><orcidid>0000-0001-8651-8844</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,1604,27924,27925</link.rule.ids><linktorsrc>$$Uhttps://dx.doi.org/10.1093/bioinformatics/btaa988$$EView_record_in_Oxford_University_Press$$FView_record_in_$$GOxford_University_Press</linktorsrc></links><search><contributor>Schwartz, Russell</contributor><creatorcontrib>Yan, Julia</creatorcontrib><creatorcontrib>Patterson, Nick</creatorcontrib><creatorcontrib>Narasimhan, Vagheesh M</creatorcontrib><title>miqoGraph: fitting admixture graphs using mixed-integer quadratic optimization</title><title>Bioinformatics (Oxford, England)</title><description>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.</description><subject>Admixtures</subject><subject>Availability</subject><subject>Bioinformatics</subject><subject>Drift</subject><subject>Genetic relationship</subject><subject>Graphs</subject><subject>Mixed integer</subject><subject>Phylogeny</subject><subject>Population genetics</subject><subject>Topology</subject><subject>Topology optimization</subject><issn>1367-4803</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><recordid>eNqNUMFKxDAQDaLguvoLUvDipe6kSdPWmyy6Cote9Bymm3TNsm26SQrq15uyi6An5zLDm_feDI-QSwo3FCo2q401XWNdi8Gs_KwOiFVZHpEJZaJIeUnp8c8M7JSceb8BgBxyMSHPrdnZhcP-_TZpTAimWyeoWvMRBqeT9bjwyeBHOIJapaYLeq1dshtQufFiYvtgWvMVZ9udk5MGt15fHPqUvD3cv84f0-XL4ml-t0xXHERIK0WhUFXGuG4Ey1HxnOYNqxAbqrXSqq5A1DQDoVgNRVEiV4ViCJjRrMw1m5LrvW_v7G7QPsjW-JXebrHTdvAy4yLnsQoeqVd_qBs7uC5-J1k0AxC0LCNL7FkrZ713upG9My26T0lBjjHL3zHLQ8xRSPdCO_T_1XwDaiWJWw</recordid><startdate>20210815</startdate><enddate>20210815</enddate><creator>Yan, Julia</creator><creator>Patterson, Nick</creator><creator>Narasimhan, Vagheesh M</creator><general>Oxford University Press</general><general>Oxford Publishing Limited (England)</general><scope>AAYXX</scope><scope>CITATION</scope><scope>7QF</scope><scope>7QO</scope><scope>7QQ</scope><scope>7SC</scope><scope>7SE</scope><scope>7SP</scope><scope>7SR</scope><scope>7TA</scope><scope>7TB</scope><scope>7TM</scope><scope>7TO</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>F28</scope><scope>FR3</scope><scope>H8D</scope><scope>H8G</scope><scope>H94</scope><scope>JG9</scope><scope>JQ2</scope><scope>K9.</scope><scope>KR7</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>P64</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0001-8651-8844</orcidid></search><sort><creationdate>20210815</creationdate><title>miqoGraph: fitting admixture graphs using mixed-integer quadratic optimization</title><author>Yan, Julia ; Patterson, Nick ; Narasimhan, Vagheesh M</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c406t-9d107d9234ef635ad4515f39aaf1eededb906b1206d3b0778a4d7d3a0a21285e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Admixtures</topic><topic>Availability</topic><topic>Bioinformatics</topic><topic>Drift</topic><topic>Genetic relationship</topic><topic>Graphs</topic><topic>Mixed integer</topic><topic>Phylogeny</topic><topic>Population genetics</topic><topic>Topology</topic><topic>Topology optimization</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yan, Julia</creatorcontrib><creatorcontrib>Patterson, Nick</creatorcontrib><creatorcontrib>Narasimhan, Vagheesh M</creatorcontrib><collection>CrossRef</collection><collection>Aluminium Industry Abstracts</collection><collection>Biotechnology Research Abstracts</collection><collection>Ceramic Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Corrosion Abstracts</collection><collection>Electronics & Communications Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Materials Business File</collection><collection>Mechanical & Transportation Engineering Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>ANTE: Abstracts in New Technology & Engineering</collection><collection>Engineering Research Database</collection><collection>Aerospace Database</collection><collection>Copper Technical Reference Library</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Materials Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Civil Engineering Abstracts</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Bioinformatics (Oxford, England)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Yan, Julia</au><au>Patterson, Nick</au><au>Narasimhan, Vagheesh M</au><au>Schwartz, Russell</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>miqoGraph: fitting admixture graphs using mixed-integer quadratic optimization</atitle><jtitle>Bioinformatics (Oxford, England)</jtitle><date>2021-08-15</date><risdate>2021</risdate><volume>37</volume><issue>16</issue><spage>2488</spage><epage>2490</epage><pages>2488-2490</pages><issn>1367-4803</issn><eissn>1367-4811</eissn><abstract>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.</abstract><cop>Oxford</cop><pub>Oxford University Press</pub><doi>10.1093/bioinformatics/btaa988</doi><tpages>3</tpages><orcidid>https://orcid.org/0000-0001-8651-8844</orcidid><oa>free_for_read</oa></addata></record> |
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| source | Access via Oxford University Press (Open Access Collection) |
| subjects | Admixtures Availability Bioinformatics Drift Genetic relationship Graphs Mixed integer Phylogeny Population genetics Topology Topology optimization |
| title | miqoGraph: fitting admixture graphs using mixed-integer quadratic optimization |
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