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<title>TreeBASE</title>

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<span id="openzim-page-title" class="mw-page-title-main"><span class="mw-page-title-main">TreeBASE</span></span>

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<p><b>TreeBASE</b><sup id="cite_ref-1" class="reference"><a href="#cite_note-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup> was a repository of <a href="Phylogenetics" title="Phylogenetics">phylogenetic</a> data published in <a href="Scientific_journal" title="Scientific journal">scientific journals</a>. In phylogenetic studies, research data are collected or generated, such as comparative observations (e.g. <a href="Maximum_parsimony_(phylogenetics)" class="mw-redirect" title="Maximum parsimony (phylogenetics)">character state matrices</a> or <a href="Multiple_sequence_alignment" title="Multiple sequence alignment">multiple sequence alignments</a>) made on a set of <a href="Taxa" class="mw-redirect" title="Taxa">taxa</a>, <a href="Metadata" title="Metadata">metadata</a> about these taxa, and the <a href="Phylogenetic_tree" title="Phylogenetic tree">phylogenetic trees</a> that are inferred to best describe the evolutionary relationships between the taxa.

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<div class="mw-heading mw-heading2"><h2 id="Mission">Mission</h2></div>

<p>The purpose of the TreeBASE project was to provide stable records and identifiers for these data, so that other workers can refer to their deposited data in their publication, and other scientists can locate the data and use them to verify the original research or to include or extend them in further analyses.

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<div class="mw-heading mw-heading2"><h2 id="History_and_funding">History and funding</h2></div>

<p>The project was started in 1994,<sup id="cite_ref-2" class="reference"><a href="#cite_note-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-3" class="reference"><a href="#cite_note-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> with funding from the US <a href="National_Science_Foundation" title="National Science Foundation">National Science Foundation</a>. After this prototype, a redesign was initiated under the CIPRES<sup id="cite_ref-4" class="reference"><a href="#cite_note-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> project. This new version was released in March 2010 and has been supported by, among others, the pPOD project,<sup id="cite_ref-5" class="reference"><a href="#cite_note-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup> which funded the addition of a <a href="RESTful" class="mw-redirect" title="RESTful">RESTful</a> web service interface with <a href="Contextual_Query_Language" title="Contextual Query Language">CQL</a> search facilities,<sup id="cite_ref-6" class="reference"><a href="#cite_note-6"><span class="cite-bracket">[</span>6<span class="cite-bracket">]</span></a></sup> and <a href="National_Evolutionary_Synthesis_Center" title="National Evolutionary Synthesis Center">National Evolutionary Synthesis Center</a> (NESCent), which hosted the database and web server.

</p><p>Starting in Winter 2010, TreeBASE was reorganized and became associated with the Phyloinformatics Research Foundation<sup id="cite_ref-7" class="reference"><a href="#cite_note-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup>

</p><p>In 2022, TreeBASE was taken offline due to security issues which were unable to be fixed with project resources; the future of the database is uncertain.<sup id="cite_ref-8" class="reference"><a href="#cite_note-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup>

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<div class="mw-heading mw-heading2"><h2 id="References">References</h2></div>

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</style><cite class="citation web cs1"><a rel="nofollow" class="external text" href="http://www.treebase.org">"TreeBASE"</a><span class="reference-accessdate">. Retrieved <span class="nowrap">5 April</span> 2011</span>.</cite></span>

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<li id="cite_note-2"><span class="mw-cite-backlink"><b><a href="#cite_ref-2">^</a></b></span> <span class="reference-text"><cite id="CITEREFSandersonM._J._DonoghueW._PielT._Eriksson1994" class="citation journal cs1">Sanderson, M. J.; M. J. Donoghue; W. Piel; T. Eriksson (1994). "TreeBASE: a prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life". <i>American Journal of Botany</i>. <b>81</b> (6): 183. <a href="JSTOR_(identifier)" class="mw-redirect" title="JSTOR (identifier)">JSTOR</a> <a rel="nofollow" class="external text" href="https://www.jstor.org/stable/2445447">2445447</a>.</cite></span>

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<li id="cite_note-3"><span class="mw-cite-backlink"><b><a href="#cite_ref-3">^</a></b></span> <span class="reference-text"><cite id="CITEREFPielM._J._DonoghueM._J._Sanderson2002" class="citation journal cs1">Piel, W. H.; M. J. Donoghue; M. J. Sanderson (2002). "TreeBASE: a database of phylogenetic knowledge". <i>To the Interoperable "Catalog of Life" with Partners Species 2000 Asia Oceanea. Research Report from the National Institute for Environmental Studies</i> (171): <span class="nowrap">41–</span>47.</cite></span>

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<li id="cite_note-4"><span class="mw-cite-backlink"><b><a href="#cite_ref-4">^</a></b></span> <span class="reference-text"><cite class="citation web cs1"><a rel="nofollow" class="external text" href="http://www.phylo.org">"CyberInfrastructure for Phylogenetic Research"</a><span class="reference-accessdate">. Retrieved <span class="nowrap">5 April</span> 2011</span>.</cite></span>

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<li id="cite_note-5"><span class="mw-cite-backlink"><b><a href="#cite_ref-5">^</a></b></span> <span class="reference-text"><cite class="citation web cs1"><a rel="nofollow" class="external text" href="http://www.phylodata.org">"processing PhylOData"</a><span class="reference-accessdate">. Retrieved <span class="nowrap">5 April</span> 2011</span>.</cite></span>

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<li id="cite_note-6"><span class="mw-cite-backlink"><b><a href="#cite_ref-6">^</a></b></span> <span class="reference-text"><cite id="CITEREFVosHilmar_LappWilliam_H._PielVal_Tannen2010" class="citation journal cs1">Vos, Rutger A.; Hilmar Lapp; William H. Piel; Val Tannen (2010). <a rel="nofollow" class="external text" href="http://hdl.handle.net/10101/npre.2010.4600.1">"TreeBASE2: Rise of the Machines"</a>. <i>Nature Precedings</i>. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.1038%2Fnpre.2010.4600">10.1038/npre.2010.4600</a></span> (inactive 1 July 2025).</cite><span class="cs1-maint citation-comment"><code class="cs1-code">{{cite journal}}</code>: CS1 maint: DOI inactive as of July 2025 (link)</span></span>

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<li id="cite_note-7"><span class="mw-cite-backlink"><b><a href="#cite_ref-7">^</a></b></span> <span class="reference-text"><cite class="citation web cs1"><a rel="nofollow" class="external text" href="http://www.phylofoundation.org">"Phyloinformatics Research Foundation"</a><span class="reference-accessdate">. Retrieved <span class="nowrap">5 April</span> 2011</span>.</cite></span>

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<li id="cite_note-8"><span class="mw-cite-backlink"><b><a href="#cite_ref-8">^</a></b></span> <span class="reference-text"><cite class="citation web cs1"><a rel="nofollow" class="external text" href="https://iphylo.blogspot.com/2022/05/thoughts-on-treebase-dying.html?fbclid=IwAR2XBtlL6KbfOfhQtut6rmahjgMyGtXXfeCCPEMm7SXLmCvBohBIRJVgG2k">"Thoughts on TreeBASE dying(?)"</a>. 11 May 2022<span class="reference-accessdate">. Retrieved <span class="nowrap">16 May</span> 2022</span>.</cite></span>

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