A good workbench for molecular and evolutionary biologists

What is it about?

Here is a short list of DAMBE functions. If it fails to drive you to sleep, then DAMBE is for you. Sequence alignment General sequence alignment with nucleotide and amino acid sequences Aligning protein-coding nucleotide sequences against aligned amino acid sequences Molecular phylogenetics Distance-based methods including neighbor-joining, Fitch-Margoliash, FastME and UPGMA, in conjunction with a variety of genetic distances including simultaneously estimated maximum composite likelihood distances, as well as a variety of distances based on nucleotide, amino acid and codon based substitution models, e.g., the distance based on the general time reversible (GTR) model for nucleotide sequences or that based on stepwise mutation model for microsatellite data. Recent update: accurate phylogenetic analysis based on pairwise alignment onyl. Maximum parsimony methods Maximum likelihood methods A versatile tree-displaying panel for exporting high-quality trees for publication Relative rate tests with nucleotide-based and codon-based models Tree-based test of the molecular clock hypothesis Dating speciation or gene duplication events with single or multiple calibration points. This includes both the regular dating with internal node calibration and tip-dating frequently used for viruses sampled at different years. Detecting recombination (Simplot, Bootscan and a new method based on compatibility matrix) Estimation of the shape parameter of the gamma distribution for rate heterogeneity the proportion of invariant sites Test substitution saturation Find best-fitting substitution models Bioinformatics tools Position weight matrix for characterizing and predicting sequence motifs Perceptron for two-group classification of sequence motifs Gibbs sampler for characterizing and predicting novel/hidden sequence motifs Hidden Markov models Secondary structure prediction tRNA anticodon identification Characterization of codon usage bias with RSCU and CAI Computing protein isoelectric point Peptide mass fingerprinting Extensive implementation of a variety of sequence formats, from the simplest FASTA format to the annotation-rich GenBank format. With the GenBank format, one can easily extract coding sequences (CDSs), exons, introns, exon-intron junctions, rRNA, tRNA, sequence upstream or downstream of CDSs, and many others.

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Why is it important?

We all need tools to do our work efficiently. DAMBE does a variety of things for research and teaching in molecular biology and evolution. Many people are using it. You will be at a terrible disadvantage if you don't.

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