{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T04:48:49Z","timestamp":1773982129873,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: The Profile Neighbor Joining (PNJ) algorithm as implemented in the software ProfDist is computationally efficient in reconstructing very large trees. Besides the huge amount of sequence data the structure is important in RNA alignment analysis and phylogenetic reconstruction.<\/jats:p><jats:p>Results: For this ProfDistS provides a phylogenetic workflow that uses individual RNA secondary structures in reconstructing phylogenies based on sequence-structure alignments\u2014using PNJ with manual or iterative and automatic profile definition. Moreover, ProfDistS can deal also with protein sequences.<\/jats:p><jats:p>Availability: ProfDistS is freely available for non-commercial use for Windows, Linux and MAC operating systems at http:\/\/profdist.bioapps.biozentrum.uni-wuerzburg.de.<\/jats:p><jats:p>Contact: \u00a0tobias.mueller@biozentrum.uni-wuerzburg.de; matthias.wolf@biozentrum.uni-wuerzburg.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn453","type":"journal-article","created":{"date-parts":[[2008,8,23]],"date-time":"2008-08-23T00:14:03Z","timestamp":1219450443000},"page":"2401-2402","source":"Crossref","is-referenced-by-count":121,"title":["ProfDistS: (profile-) distance based phylogeny on sequence\u2014structure alignments"],"prefix":"10.1093","volume":"24","author":[{"given":"Matthias","family":"Wolf","sequence":"first","affiliation":[{"name":"1 Department of Bioinformatics, Biocenter, University of W\u00fcrzburg, Am Hubland, 97074 W\u00fcrzburg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benjamin","family":"Ruderisch","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, Biocenter, University of W\u00fcrzburg, Am Hubland, 97074 W\u00fcrzburg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Dandekar","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, Biocenter, University of W\u00fcrzburg, Am Hubland, 97074 W\u00fcrzburg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00f6rg","family":"Schultz","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, Biocenter, University of W\u00fcrzburg, Am Hubland, 97074 W\u00fcrzburg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tobias","family":"M\u00fcller","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, Biocenter, University of W\u00fcrzburg, Am Hubland, 97074 W\u00fcrzburg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,8,21]]},"reference":[{"key":"2023020211253039900_B1","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1186\/1471-2105-8-271","article-title":"Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization","volume":"8","author":"Bauer","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023020211253039900_B2","doi-asserted-by":"crossref","first-page":"2108","DOI":"10.1093\/bioinformatics\/bti289","article-title":"ProfDist: a tool for the construction of large phylogenetic trees based on profile distances","volume":"21","author":"Friedrich","year":"2005","journal-title":"Bionformatics"},{"key":"2023020211253039900_B3","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1093\/oxfordjournals.molbev.a025808","article-title":"BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data","volume":"14","author":"Gascuel","year":"1997","journal-title":"Mol. 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