{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T09:23:08Z","timestamp":1770888188086,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: With the explosive growth of bacterial and archaeal sequence data, large-scale phylogenetic analyses present both opportunities and challenges. Here we describe AMPHORA2, an automated phylogenomic inference tool that can be used for high-throughput, high-quality genome tree reconstruction and metagenomic phylotyping. Compared with its predecessor, AMPHORA2 has several major enhancements and new functions: it has a greatly expanded phylogenetic marker database and can analyze both bacterial and archaeal sequences; it incorporates probability-based sequence alignment masks that improve the phylogenetic accuracy; it can analyze DNA as well as protein sequences and is more sensitive in marker identification; finally, it is over 100\u00d7 faster in metagenomic phylotyping.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/wolbachia.biology.virginia.edu\/WuLab\/Software.html.<\/jats:p>\n               <jats:p>Contact: \u00a0mw4yv@virginia.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts079","type":"journal-article","created":{"date-parts":[[2012,2,14]],"date-time":"2012-02-14T01:23:09Z","timestamp":1329182589000},"page":"1033-1034","source":"Crossref","is-referenced-by-count":424,"title":["Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2"],"prefix":"10.1093","volume":"28","author":[{"given":"Martin","family":"Wu","sequence":"first","affiliation":[{"name":"1 Department of Biology, University of Virginia, Charlottesville, VA 22904, USA"}]},{"given":"Alexandra J.","family":"Scott","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2012,2,12]]},"reference":[{"key":"2023012512215201300_B1","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1093\/sysbio\/syr010","article-title":"Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood","volume":"60","author":"Berger","year":"2011","journal-title":"Systematic Biol."},{"key":"2023012512215201300_B2","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1101\/gr.8.3.163","article-title":"Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis","volume":"8","author":"Eisen","year":"1998","journal-title":"Genome Res."},{"key":"2023012512215201300_B3","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1093\/nar\/30.7.1575","article-title":"An efficient algorithm for large-scale detection of protein families","volume":"30","author":"Enright","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023012512215201300_B4","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1038\/361023b0","article-title":"Ribosomal RNA trees misleading?","volume":"361","author":"Hasegawa","year":"1993","journal-title":"Nature"},{"key":"2023012512215201300_B5","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1016\/j.syapm.2010.03.003","article-title":"En route to a genome-based classification of Archaea and Bacteria?","volume":"33","author":"Klenk","year":"2010","journal-title":"Syst. 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