DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites. (May 2010)

• Record Type: Journal Article
• Authors: Deng, Wenjie; Maust, Brandon S.; Nickle, David C.; Learn, Gerald H.; Liu, Yi; Heath, Laura; Kosakovsky Pond, Sergei L; Mullins, James I.
• Is Part Of: Biotechniques. Volume 48:Number 5(2010)
• Page Start: 405
• Page End: 408
• Publication Date: 2010-05
• Subjects: phylogeny -- divergence -- diversity -- informative sites -- center of tree -- maximum likelihood; Biology, Experimental -- Periodicals; Molecular biology -- Periodicals; Medical technology -- Periodicals; Biology, Experimental; Medical technology; Molecular biology; Clinical Laboratory Techniques -- Periodicals; Research -- Periodicals; Medical Laboratory Science -- Periodicals; Periodicals; Electronic journals; 570
• DOI: 10.2144/000113370
• Languages: English
• ISSNs: 0736-6205

Abstract

DIVEIN is a web interface that performs automated phylogenetic and other analyses of nucleotide and amino acid sequences. Starting with a set of aligned sequences, DIVEIN estimates evolutionary parameters and phylogenetic trees while allowing the user to choose from a variety of evolutionary models; it then reconstructs the consensus (CON), most recent common ancestor (MRCA), and center of tree (COT) sequences. DIVEIN also provides tools for further analyses, including condensing sequence alignments to show only informative sites or private mutations; computing phylogenetic or pairwise divergence from any user-specified sequence (CON, MRCA, COT, or existing sequence from the alignment); computing and outputting all genetic distances in column format; calculating summary statistics of diversity and divergence from pairwise distances; and graphically representing the inferred tree and plots of divergence, diversity, and distance distribution histograms. DIVEIN is available athttp://indra.mullins.microbiol.washington.edu/DIVEIN .