title: DAMBE6: New Tools for Microbial Genomics, Phylogenetics, and Molecular Evolution.
abstract: DAMBE is a comprehensive software workbench for data analysis in molecular biology, phylogenetics, and evolution. Several important new functions have been added since version 5 of DAMBE: 1) comprehensive genomic profiling of translation initiation efficiency of different genes in different prokaryotic species, 2) a new index of translation elongation (ITE) that takes into account both tRNA-mediated selection and background mutation on codon-anticodon adaptation, 3) a new and accurate phylogenetic approach based on pairwise alignment only, which is useful for highly divergent sequences from which a reliable multiple sequence alignment is difficult to obtain. Many other functions have been updated and improved including PWM for motif characterization, Gibbs sampler for de novo motif discovery, hidden Markov models for protein secondary structure prediction, self-organizing map for nonlinear clustering of transcriptomic data, comprehensive sequence alignment, and phylogenetic functions. DAMBE features a graphic, user-friendly and intuitive interface, and is freely available from http://dambe.bio.uottawa.ca.
authors.affiliation: From the Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, 30 Marie Curie, PO Box 450, Station A, Ottawa, ON K1N 6N5, Canada.
authors.forename: Xuhua
authors.initials: X
authors.lastname: Xia
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D019143:Evolution, Molecular; D064349:Genome, Microbial; D023281:Genomics / Q000379:methods*; D010441:Peptide Chain Elongation, Translational; D010442:Peptide Chain Initiation, Translational; D010802:Phylogeny; D016415:Sequence Alignment; D012984:Software; D059467:Transcriptome
keywords: bioinformatics; genomics; index of translation elongation; phylogenetic analysis based on pairwise alignment; translation initiation analysis