{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T19:10:09Z","timestamp":1675192209789},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: A phenotypic character has a convex mapping to a given phylogenetic tree if each character state can be assigned a single point of origin in the tree. However, phenomena such as convergent evolution and lateral genetic transfer can lead to intermingling of character states and a consequent non-convex mapping. The phylogenetic heterogeneity of different characters can identify subsets of states that are non-randomly associated or which may have been transferred from one lineage to another. We have developed Radi\u00e9, an interactive 3D Java application for mapping character states to the leaves and internal edges of a radial phylogenetic tree. In Radi\u00e9 each state of a given character is associated with a unique color, and internal edges with many descendant character states can be represented in a number of different ways to illustrate the diversity within each group.<\/jats:p>\n               <jats:p>Availability: Radi\u00e9 is freely available for download at http:\/\/kiwi.cs.dal.ca\/~beiko\/software-and-data\/radie; source code is available upon request from the authors.<\/jats:p>\n               <jats:p>Contact: \u00a0beiko@cs.dal.ca<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp044","type":"journal-article","created":{"date-parts":[[2009,2,5]],"date-time":"2009-02-05T01:56:04Z","timestamp":1233798964000},"page":"672-673","source":"Crossref","is-referenced-by-count":0,"title":["Radi\u00e9: visualizing taxon properties and parsimonious mappings using a radial phylogenetic tree"],"prefix":"10.1093","volume":"25","author":[{"given":"Jacqueline","family":"Whalley","sequence":"first","affiliation":[{"name":"1 School of Computing and Mathematical Sciences, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand and 2Faculty of Computer Science, Dalhousie University, 6050 University Avenue, Halifax, Nova Scotia, Canada B3H 1W5"}]},{"given":"Stephen","family":"Brooks","sequence":"additional","affiliation":[{"name":"1 School of Computing and Mathematical Sciences, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand and 2Faculty of Computer Science, Dalhousie University, 6050 University Avenue, Halifax, Nova Scotia, Canada B3H 1W5"}]},{"given":"Robert G.","family":"Beiko","sequence":"additional","affiliation":[{"name":"1 School of Computing and Mathematical Sciences, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand and 2Faculty of Computer Science, Dalhousie University, 6050 University Avenue, Halifax, Nova Scotia, Canada B3H 1W5"}]}],"member":"286","published-online":{"date-parts":[[2009,2,4]]},"reference":[{"key":"2023013110114023500_B1","doi-asserted-by":"crossref","first-page":"14332","DOI":"10.1073\/pnas.0504068102","article-title":"Highways of gene sharing in prokaryotes","volume":"104","author":"Beiko","year":"2005","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013110114023500_B2","doi-asserted-by":"crossref","first-page":"406","DOI":"10.2307\/2412116","article-title":"Toward defining the course of evolution: minimum change for a specified tree topology","volume":"20","author":"Fitch","year":"1971","journal-title":"Syst. Zool."},{"key":"2023013110114023500_B3","doi-asserted-by":"crossref","first-page":"6688","DOI":"10.1093\/nar\/gkn668","article-title":"Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world","volume":"36","author":"Koonin","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023013110114023500_B4","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1093\/bioinformatics\/btl529","article-title":"Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation","volume":"23","author":"Letunic","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013110114023500_B5","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1093\/sysbio\/46.4.590","article-title":"NEXUS: an extensible file format for systematic information","volume":"46","author":"Maddison","year":"1997","journal-title":"Syst. Biol."},{"key":"2023013110114023500_B6","first-page":"3","article-title":"The bacterium's place in nature","volume-title":"Microbial Phylogeny and Evolution: Concepts and Controversies.","author":"Sapp","year":"2005"},{"key":"2023013110114023500_B7","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1126\/science.1071196","article-title":"Rooting the eukaryote tree by using a derived gene fusion","volume":"297","author":"Stechmann","year":"2002","journal-title":"Science"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/5\/672\/48984414\/bioinformatics_25_5_672.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/5\/672\/48984414\/bioinformatics_25_5_672.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T18:28:08Z","timestamp":1675189688000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/5\/672\/183817"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,2,4]]},"references-count":7,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2009,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp044","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,3,1]]},"published":{"date-parts":[[2009,2,4]]}}}