HAlign 3: Fast Multiple Alignment of Ultra-Large Numbers of Similar DNA/RNA Sequences
Abstract HAlign is a cross-platform program that performs multiple sequence alignments based on the center star strategy. Here we present two major updates of HAlign 3, which helped improve the time efficiency and the alignment quality, and made HAlign 3 a specialized program to process ultra-large...
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| Veröffentlicht in: | Molecular biology and evolution 2022-08, Vol.39 (8) |
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| container_title | Molecular biology and evolution |
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| creator | Tang, Furong Chao, Jiannan Wei, Yanming Yang, Fenglong Zhai, Yixiao Xu, Lei Zou, Quan |
| description | Abstract
HAlign is a cross-platform program that performs multiple sequence alignments based on the center star strategy. Here we present two major updates of HAlign 3, which helped improve the time efficiency and the alignment quality, and made HAlign 3 a specialized program to process ultra-large numbers of similar DNA/RNA sequences, such as closely related viral or prokaryotic genomes. HAlign 3 can be easily installed via the Anaconda and Java release package on macOS, Linux, Windows subsystem for Linux, and Windows systems, and the source code is available on GitHub (https://github.com/malabz/HAlign-3). |
| doi_str_mv | 10.1093/molbev/msac166 |
| format | Article |
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HAlign is a cross-platform program that performs multiple sequence alignments based on the center star strategy. Here we present two major updates of HAlign 3, which helped improve the time efficiency and the alignment quality, and made HAlign 3 a specialized program to process ultra-large numbers of similar DNA/RNA sequences, such as closely related viral or prokaryotic genomes. HAlign 3 can be easily installed via the Anaconda and Java release package on macOS, Linux, Windows subsystem for Linux, and Windows systems, and the source code is available on GitHub (https://github.com/malabz/HAlign-3).</description><identifier>ISSN: 0737-4038</identifier><identifier>EISSN: 1537-1719</identifier><identifier>DOI: 10.1093/molbev/msac166</identifier><identifier>PMID: 35915051</identifier><language>eng</language><publisher>Oxford University Press</publisher><subject>Genomes ; Genomics ; Resources ; Statistics</subject><ispartof>Molecular biology and evolution, 2022-08, Vol.39 (8)</ispartof><rights>The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. 2022</rights><rights>COPYRIGHT 2022 Oxford University Press</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c440t-38d36957eaf835d5cef2d97896979c0fd1908f253621aad5da824bcc35730b463</citedby><cites>FETCH-LOGICAL-c440t-38d36957eaf835d5cef2d97896979c0fd1908f253621aad5da824bcc35730b463</cites><orcidid>0000-0003-2040-3731 ; 0000-0001-6406-1142 ; 0000-0001-7546-7500</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9372455/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9372455/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,1604,27924,27925,53791,53793</link.rule.ids></links><search><contributor>Crandall, Keith</contributor><creatorcontrib>Tang, Furong</creatorcontrib><creatorcontrib>Chao, Jiannan</creatorcontrib><creatorcontrib>Wei, Yanming</creatorcontrib><creatorcontrib>Yang, Fenglong</creatorcontrib><creatorcontrib>Zhai, Yixiao</creatorcontrib><creatorcontrib>Xu, Lei</creatorcontrib><creatorcontrib>Zou, Quan</creatorcontrib><title>HAlign 3: Fast Multiple Alignment of Ultra-Large Numbers of Similar DNA/RNA Sequences</title><title>Molecular biology and evolution</title><description>Abstract
HAlign is a cross-platform program that performs multiple sequence alignments based on the center star strategy. Here we present two major updates of HAlign 3, which helped improve the time efficiency and the alignment quality, and made HAlign 3 a specialized program to process ultra-large numbers of similar DNA/RNA sequences, such as closely related viral or prokaryotic genomes. HAlign 3 can be easily installed via the Anaconda and Java release package on macOS, Linux, Windows subsystem for Linux, and Windows systems, and the source code is available on GitHub (https://github.com/malabz/HAlign-3).</description><subject>Genomes</subject><subject>Genomics</subject><subject>Resources</subject><subject>Statistics</subject><issn>0737-4038</issn><issn>1537-1719</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><recordid>eNqFUU1vEzEUtBCIpoUrZx_hsI29_lpzQFoVSpFCKrXkbHm9djCy18HercS_r0siECf0Du9p3sxopAHgDUaXGEmyjikM9mEdizaY82dghRkRDRZYPgcrJOpNEenOwHkpPxDClHL-EpwRJjFDDK_A7qYPfj9B8h5e6zLDr0uY_SFY-BuOdpphcnAX5qybjc57C7dLHGwuT_C9jz7oDD9u-_Xdtof39udiJ2PLK_DC6VDs69O-ALvrT9-ubprN7ecvV_2mMZSiuSHdSLhkwmrXETYyY107StFJLoU0yI1Yos61jPAWaz2yUXctHYwhTBA0UE4uwIej72EZoh1NjZt1UIfso86_VNJe_fuZ_He1Tw9KEtFSxqrB25NBTjV7mVX0xdgQ9GTTUlRbkxAukJCVenmk7nWwyk8uVUdTZ7TRmzRZ5yveC0GpoKwVfwUmp1KydX9yYaSeylPH8tSpvCp4dxSk5fA_7iPpNptd</recordid><startdate>20220803</startdate><enddate>20220803</enddate><creator>Tang, Furong</creator><creator>Chao, Jiannan</creator><creator>Wei, Yanming</creator><creator>Yang, Fenglong</creator><creator>Zhai, Yixiao</creator><creator>Xu, Lei</creator><creator>Zou, Quan</creator><general>Oxford University Press</general><scope>TOX</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-2040-3731</orcidid><orcidid>https://orcid.org/0000-0001-6406-1142</orcidid><orcidid>https://orcid.org/0000-0001-7546-7500</orcidid></search><sort><creationdate>20220803</creationdate><title>HAlign 3: Fast Multiple Alignment of Ultra-Large Numbers of Similar DNA/RNA Sequences</title><author>Tang, Furong ; Chao, Jiannan ; Wei, Yanming ; Yang, Fenglong ; Zhai, Yixiao ; Xu, Lei ; Zou, Quan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c440t-38d36957eaf835d5cef2d97896979c0fd1908f253621aad5da824bcc35730b463</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Genomes</topic><topic>Genomics</topic><topic>Resources</topic><topic>Statistics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Tang, Furong</creatorcontrib><creatorcontrib>Chao, Jiannan</creatorcontrib><creatorcontrib>Wei, Yanming</creatorcontrib><creatorcontrib>Yang, Fenglong</creatorcontrib><creatorcontrib>Zhai, Yixiao</creatorcontrib><creatorcontrib>Xu, Lei</creatorcontrib><creatorcontrib>Zou, Quan</creatorcontrib><collection>Access via Oxford University Press (Open Access Collection)</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Molecular biology and evolution</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Tang, Furong</au><au>Chao, Jiannan</au><au>Wei, Yanming</au><au>Yang, Fenglong</au><au>Zhai, Yixiao</au><au>Xu, Lei</au><au>Zou, Quan</au><au>Crandall, Keith</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>HAlign 3: Fast Multiple Alignment of Ultra-Large Numbers of Similar DNA/RNA Sequences</atitle><jtitle>Molecular biology and evolution</jtitle><date>2022-08-03</date><risdate>2022</risdate><volume>39</volume><issue>8</issue><issn>0737-4038</issn><eissn>1537-1719</eissn><abstract>Abstract
HAlign is a cross-platform program that performs multiple sequence alignments based on the center star strategy. Here we present two major updates of HAlign 3, which helped improve the time efficiency and the alignment quality, and made HAlign 3 a specialized program to process ultra-large numbers of similar DNA/RNA sequences, such as closely related viral or prokaryotic genomes. HAlign 3 can be easily installed via the Anaconda and Java release package on macOS, Linux, Windows subsystem for Linux, and Windows systems, and the source code is available on GitHub (https://github.com/malabz/HAlign-3).</abstract><pub>Oxford University Press</pub><pmid>35915051</pmid><doi>10.1093/molbev/msac166</doi><orcidid>https://orcid.org/0000-0003-2040-3731</orcidid><orcidid>https://orcid.org/0000-0001-6406-1142</orcidid><orcidid>https://orcid.org/0000-0001-7546-7500</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Molecular biology and evolution, 2022-08, Vol.39 (8) |
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| source | DOAJ Directory of Open Access Journals; Access via Oxford University Press (Open Access Collection); EZB-FREE-00999 freely available EZB journals; PubMed Central; Alma/SFX Local Collection; Free Full-Text Journals in Chemistry |
| subjects | Genomes Genomics Resources Statistics |
| title | HAlign 3: Fast Multiple Alignment of Ultra-Large Numbers of Similar DNA/RNA Sequences |
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