iTUPA: an online automated application to perform Topographic-Unit Parsimony Analysis
Abstract Summary iTUPA is a free online application for automatizing the Topographic-Unit Parsimony Analysis (TUPA), which identifies areas of endemism based on topography. iTUPA generates species-occurrences matrices based on user-defined topographic units (TUs) and provides a parsimony analysis of...
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| Veröffentlicht in: | Bioinformatics 2019-11, Vol.35 (22), p.4818-4820 |
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| container_title | Bioinformatics |
| container_volume | 35 |
| creator | Hammoud, Muhsen Santos, Charles Morphy D Gois, João Paulo |
| description | Abstract
Summary
iTUPA is a free online application for automatizing the Topographic-Unit Parsimony Analysis (TUPA), which identifies areas of endemism based on topography. iTUPA generates species-occurrences matrices based on user-defined topographic units (TUs) and provides a parsimony analysis of the generated matrix. We tested iTUPA after a proposal of regionalization for the Brazilian Atlantic Forest. iTUPA can handle millions of species registers simultaneously and uses Google Earth high-definition maps to visually explore the endemism data. We believe iTUPA is a useful tool for further discussions on biodiversity conservation.
Availability and implementation
iTUPA is hosted on Google cloud and freely available at http://nuvem.ufabc.edu.br/itupa. iTUPA is implemented using R (version 3.5.1), with RStudio 1.1.453 used as the implementation IDE, Shiny 1.1.0 web framework, and Google Maps® API version 3.36. |
| doi_str_mv | 10.1093/bioinformatics/btz487 |
| format | Article |
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Summary
iTUPA is a free online application for automatizing the Topographic-Unit Parsimony Analysis (TUPA), which identifies areas of endemism based on topography. iTUPA generates species-occurrences matrices based on user-defined topographic units (TUs) and provides a parsimony analysis of the generated matrix. We tested iTUPA after a proposal of regionalization for the Brazilian Atlantic Forest. iTUPA can handle millions of species registers simultaneously and uses Google Earth high-definition maps to visually explore the endemism data. We believe iTUPA is a useful tool for further discussions on biodiversity conservation.
Availability and implementation
iTUPA is hosted on Google cloud and freely available at http://nuvem.ufabc.edu.br/itupa. iTUPA is implemented using R (version 3.5.1), with RStudio 1.1.453 used as the implementation IDE, Shiny 1.1.0 web framework, and Google Maps® API version 3.36.</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1460-2059</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btz487</identifier><identifier>PMID: 31197309</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><ispartof>Bioinformatics, 2019-11, Vol.35 (22), p.4818-4820</ispartof><rights>The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2019</rights><rights>The Author(s) (2019). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c350t-f474e2c1ba6e557455f1462a884894823e459ac561e42cde571b5f02ca8e02113</citedby><cites>FETCH-LOGICAL-c350t-f474e2c1ba6e557455f1462a884894823e459ac561e42cde571b5f02ca8e02113</cites><orcidid>0000-0002-9460-3085</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,1603,27923,27924</link.rule.ids><linktorsrc>$$Uhttps://dx.doi.org/10.1093/bioinformatics/btz487$$EView_record_in_Oxford_University_Press$$FView_record_in_$$GOxford_University_Press</linktorsrc><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31197309$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Schwartz, Russell</contributor><creatorcontrib>Hammoud, Muhsen</creatorcontrib><creatorcontrib>Santos, Charles Morphy D</creatorcontrib><creatorcontrib>Gois, João Paulo</creatorcontrib><title>iTUPA: an online automated application to perform Topographic-Unit Parsimony Analysis</title><title>Bioinformatics</title><addtitle>Bioinformatics</addtitle><description>Abstract
Summary
iTUPA is a free online application for automatizing the Topographic-Unit Parsimony Analysis (TUPA), which identifies areas of endemism based on topography. iTUPA generates species-occurrences matrices based on user-defined topographic units (TUs) and provides a parsimony analysis of the generated matrix. We tested iTUPA after a proposal of regionalization for the Brazilian Atlantic Forest. iTUPA can handle millions of species registers simultaneously and uses Google Earth high-definition maps to visually explore the endemism data. We believe iTUPA is a useful tool for further discussions on biodiversity conservation.
Availability and implementation
iTUPA is hosted on Google cloud and freely available at http://nuvem.ufabc.edu.br/itupa. iTUPA is implemented using R (version 3.5.1), with RStudio 1.1.453 used as the implementation IDE, Shiny 1.1.0 web framework, and Google Maps® API version 3.36.</description><issn>1367-4803</issn><issn>1460-2059</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><recordid>eNqNkD1PwzAURS0EoqXwE0AeWUL9GSdsVcWXVIkOyRw5rgNGiW3sZCi_nlQpSGxM7w33nvd0ALjG6A6jnC5r44xtXOhkb1Rc1v0Xy8QJmGOWooQgnp-OO01FwjJEZ-Aixg-EOGaMnYMZxTgXFOVzUJqi3K7uobTQ2dZYDeXQuxGqd1B63xo18p2FvYNeh8M9WDjv3oL070YlpTU93MoQTefsHq6sbPfRxEtw1sg26qvjXIDy8aFYPyeb16eX9WqTKMpRnzRMME0UrmWqOReM82Z8n8gsY1nOMkI147lUPMWaEbXTXOCaN4gomWlEMKYLcDtxfXCfg4591ZmodNtKq90QK0Ix44ILRMcon6IquBiDbiofTCfDvsKoOhit_hqtJqNj7-Z4Yqg7vftt_SgcA2gKuMH_k_kNpYuI8A</recordid><startdate>20191101</startdate><enddate>20191101</enddate><creator>Hammoud, Muhsen</creator><creator>Santos, Charles Morphy D</creator><creator>Gois, João Paulo</creator><general>Oxford University Press</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-9460-3085</orcidid></search><sort><creationdate>20191101</creationdate><title>iTUPA: an online automated application to perform Topographic-Unit Parsimony Analysis</title><author>Hammoud, Muhsen ; Santos, Charles Morphy D ; Gois, João Paulo</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c350t-f474e2c1ba6e557455f1462a884894823e459ac561e42cde571b5f02ca8e02113</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hammoud, Muhsen</creatorcontrib><creatorcontrib>Santos, Charles Morphy D</creatorcontrib><creatorcontrib>Gois, João Paulo</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Hammoud, Muhsen</au><au>Santos, Charles Morphy D</au><au>Gois, João Paulo</au><au>Schwartz, Russell</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>iTUPA: an online automated application to perform Topographic-Unit Parsimony Analysis</atitle><jtitle>Bioinformatics</jtitle><addtitle>Bioinformatics</addtitle><date>2019-11-01</date><risdate>2019</risdate><volume>35</volume><issue>22</issue><spage>4818</spage><epage>4820</epage><pages>4818-4820</pages><issn>1367-4803</issn><eissn>1460-2059</eissn><eissn>1367-4811</eissn><abstract>Abstract
Summary
iTUPA is a free online application for automatizing the Topographic-Unit Parsimony Analysis (TUPA), which identifies areas of endemism based on topography. iTUPA generates species-occurrences matrices based on user-defined topographic units (TUs) and provides a parsimony analysis of the generated matrix. We tested iTUPA after a proposal of regionalization for the Brazilian Atlantic Forest. iTUPA can handle millions of species registers simultaneously and uses Google Earth high-definition maps to visually explore the endemism data. We believe iTUPA is a useful tool for further discussions on biodiversity conservation.
Availability and implementation
iTUPA is hosted on Google cloud and freely available at http://nuvem.ufabc.edu.br/itupa. iTUPA is implemented using R (version 3.5.1), with RStudio 1.1.453 used as the implementation IDE, Shiny 1.1.0 web framework, and Google Maps® API version 3.36.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>31197309</pmid><doi>10.1093/bioinformatics/btz487</doi><tpages>3</tpages><orcidid>https://orcid.org/0000-0002-9460-3085</orcidid></addata></record> |
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| source | Oxford Journals Open Access Collection |
| title | iTUPA: an online automated application to perform Topographic-Unit Parsimony Analysis |
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