{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T07:29:27Z","timestamp":1776929367361,"version":"3.51.2"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Phylogenetics, or reconstructing the evolutionary relationships of organisms, is critical for understanding evolution. A large number of heuristic algorithms for phylogenetics have been developed, some of which enable estimates of trees with tens of thousands of taxa. Such trees may not be robust, as small changes in the input data can cause major differences in the optimal topology. Tools that can assess the quality and stability of phylogenetic tree estimates and identify the most reliable parts of the tree are needed.<\/jats:p>\n               <jats:p>Results: We define measures that assess the stability of trees, subtrees and individual taxa with respect to changes in the input sequences. Our measures consider changes at the finest granularity in the input data (i.e. individual nucleotides). We demonstrate the effectiveness of our measures on large published datasets. Our measures are computationally feasible for phylogenetic datasets consisting of tens of thousands of taxa.<\/jats:p>\n               <jats:p>Availability: This software is available at http:\/\/bioinformatics.cise.ufl.edu\/phylostab<\/jats:p>\n               <jats:p>Contact: \u00a0sheikh@cise.ufl.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts657","type":"journal-article","created":{"date-parts":[[2012,11,19]],"date-time":"2012-11-19T01:40:30Z","timestamp":1353289230000},"page":"166-174","source":"Crossref","is-referenced-by-count":6,"title":["Stability analysis of phylogenetic trees"],"prefix":"10.1093","volume":"29","author":[{"given":"Saad I.","family":"Sheikh","sequence":"first","affiliation":[{"name":"1 Department of Computer and Information Science and Engineering, University of Florida, FL, 32611 USA and 2Department of Biology, University of Florida, FL, 32611 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tamer","family":"Kahveci","sequence":"additional","affiliation":[{"name":"1 Department of Computer and Information Science and Engineering, University of Florida, FL, 32611 USA and 2Department of Biology, University of Florida, FL, 32611 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sanjay","family":"Ranka","sequence":"additional","affiliation":[{"name":"1 Department of Computer and Information Science and Engineering, University of Florida, FL, 32611 USA and 2Department of Biology, University of Florida, FL, 32611 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J.","family":"Gordon Burleigh","sequence":"additional","affiliation":[{"name":"1 Department of Computer and Information Science and Engineering, University of Florida, FL, 32611 USA and 2Department of Biology, University of Florida, FL, 32611 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,11,18]]},"reference":[{"key":"2023012810150205100_bts657-B1","doi-asserted-by":"crossref","DOI":"10.1109\/BIBM.2011.70","article-title":"A simple and accurate method for rogue taxon identification","volume-title":"Proceedings of IEEE BIBM 2011","author":"Aberer","year":"2011"},{"key":"2023012810150205100_bts657-B2","article-title":"RogueNaRok: an efficient and exact algorithm for rogue taxon identification","author":"Aberer","year":"2011","journal-title":"Technical Report Exelixis-RRDR-2011-10"},{"key":"2023012810150205100_bts657-B3","doi-asserted-by":"crossref","first-page":"795","DOI":"10.2307\/2408870","article-title":"The limit of amino acid sequence data in angiosperm phylogenetic reconstruction","volume":"42","author":"Bremer","year":"1988","journal-title":"Evolution"},{"key":"2023012810150205100_bts657-B4","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1111\/j.1096-0031.1994.tb00179.x","article-title":"Branch support and tree stability","volume":"10","author":"Bremer","year":"1994","journal-title":"Cladistics"},{"key":"2023012810150205100_bts657-B5","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1098\/rstb.1996.0107","article-title":"Phylogenetic uncertainties and sensitivity analyses in comparative biology","volume":"351","author":"Donoghue","year":"1996","journal-title":"Philos. 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