XiaLab at University of Ottawa

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DAMBE (Windows, MAC and Linux)

Installation packages

Microsoft Windows
Macintosh (missing some advanced functions in the Windows version)
Linux (missing some advanced functions in the Windows version)

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Lab manual for teaching

New Citation:

Xia X. 2017. DAMBE6: New tools for microbial genomics, phylogenetics and molecular evolution. J Hered esx033. doi: 10.1093/jhered/esx033

Xia, X. 2013. DAMBE5: A comprehensive software package for data analysis in molecular biology and evolution. Molecular Biology and Evolution 30:1720-1728

Summary of DAMBE functions:

  1. Sequence alignment
    • General sequence alignment with nucleotide and amino acid sequences
    • Aligning protein-coding nucleotide sequences against aligned amino acid sequences
  2. 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
  3. 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
  4. 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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