{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T03:27:22Z","timestamp":1764905242320},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: \u00a0Paloverde is a new program designed to help visualize the phylogenetic structure of moderately large trees\u2014trees on the scale of 100\u20132500 leaf nodes. The program embeds the user in an interactive virtual 3D world in which a large tree presented in various layouts can be manipulated through a mouse interface. The program implements radial 2D layouts, and true 3D spiral, conical and hemispherical (i.e. truly \u2018tree\u2019-like) layouts. Subclades can be defined in the input file (using standard node-based definitions) and displayed collapsed as new leaf nodes, or left intact but annotated with names around the periphery of the tree. A search tool lets the user zoom to any selected leaf node. Paloverde is an open source project written in ANSI C using the OpenGL library for 3D visualization.<\/jats:p>\n               <jats:p>Availability: Source code, makefiles for Mac OS X and Linux and a compiled binary for Mac OS X are available at , along with a sample dataset.<\/jats:p>\n               <jats:p>Contact: \u00a0mjsanderson@ucdavis.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl044","type":"journal-article","created":{"date-parts":[[2006,2,25]],"date-time":"2006-02-25T01:14:23Z","timestamp":1140830063000},"page":"1004-1006","source":"Crossref","is-referenced-by-count":18,"title":["<i>Paloverde<\/i>: an OpenGL 3D phylogeny browser"],"prefix":"10.1093","volume":"22","author":[{"given":"Michael J.","family":"Sanderson","sequence":"first","affiliation":[{"name":"Section of Evolution and Ecology, University of California \u00a0 Davis, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,2,24]]},"reference":[{"key":"2023012409150380500_b1","doi-asserted-by":"crossref","first-page":"660","DOI":"10.1093\/bioinformatics\/16.7.660","article-title":"Visualizing large hierarchical clusters in hyperbolic space","volume":"16","author":"Bingham","year":"2000","journal-title":"Bioinformatics"},{"key":"2023012409150380500_b2","doi-asserted-by":"crossref","first-page":"660","DOI":"10.1080\/10635150590947104","article-title":"Automated phylogenetic taxonomy: an example in the Homobasidiomycetes (mushroom-forming fungi)","volume":"54","author":"Hibbett","year":"2005","journal-title":"Syst. 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Phylogenetic Analysis Using Parsimony (*and Other Methods)","author":"Swofford","year":"2002"},{"key":"2023012409150380500_b9","doi-asserted-by":"crossref","first-page":"3801","DOI":"10.1093\/bioinformatics\/bti590","article-title":"Phylogenetic trees: visualizing, customizing and detecting incongruence","volume":"21","author":"Trooskens","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012409150380500_b10","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1093\/bioinformatics\/17.4.383","article-title":"ATV: display and manipulation of annotated phylogenetic trees","volume":"17","author":"Zmasek","year":"2001","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/8\/1004\/48841134\/bioinformatics_22_8_1004.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/8\/1004\/48841134\/bioinformatics_22_8_1004.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T09:23:08Z","timestamp":1674552188000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/8\/1004\/227412"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,2,24]]},"references-count":10,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2006,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl044","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,4,15]]},"published":{"date-parts":[[2006,2,24]]}}}