title: DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites.
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 at http://indra.mullins.microbiol.washington.edu/DIVEIN.
authors.affiliation: Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA.
authors.forename: Wenjie
authors.initials: W
authors.lastname: Deng
authors.forename: Brandon S
authors.initials: BS
authors.lastname: Maust
authors.forename: David C
authors.initials: DC
authors.lastname: Nickle
authors.forename: Gerald H
authors.initials: GH
authors.lastname: Learn
authors.forename: Yi
authors.initials: Y
authors.lastname: Liu
authors.forename: Laura
authors.initials: L
authors.lastname: Heath
authors.forename: Sergei L
authors.initials: SL
authors.lastname: Kosakovsky Pond
authors.forename: James I
authors.initials: JI
authors.lastname: Mullins
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D014644:Genetic Variation; D020407:Internet; D010802:Phylogeny; D014584:User-Computer Interface