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.

Figure 1

Screen shots of phylogeny/divergence/diversity output in DIVEIN. (A) Parameter settings for running the program. (B) Phylogenetic tree viewed through the Archaeopteryx Java applet. (C) Estimated evolutionary parameters. (D) Reconstructed MRCA sequence. (E) Summarized distances between groups. (F) Summarized divergence from MRCA for each group. (G) Divergence plot generated by clicking the Draw divergence chart button. (H) Summarized diversity for each group. (I) Diversity plot generated by clicking the Draw diversity chart button. (J) Distance matrix. (K) Distance distribution histogram generated by clicking the Draw histogram button.