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DAMBE

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Here is a short 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 conjuction 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.
    • 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
    • Estimation of
      • the shape parameter of the gamma distribution for rate heterogeneity
      • the proportion of invariate 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.

Application Details:

Developer: Xuhua Xia
URL: http://dambe.bio.uottawa.ca/da...

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VersionDescriptionLatest RatingLatest Wine version testedTest resultsComments
5.05most recent versionPlatinum1.1.1310
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