Docs 2020.6.30a
  • Install
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        • Tutorials
          • Data manipulation
          • General data analysis
          • Modelling Evolution
          • Phylogenetic Reconstruction

    Tutorials¶

    Note

    See Data Files Used in the Documentation for data the files used.

    Data manipulation¶

    • Advanced sequence handling
    • Annotating alignments and sequences
    • Map protein alignment gaps to DNA alignment gaps
    • Manipulation of Tree Node Objects
    • An Example of Conditional Tree Node Modifications

    General data analysis¶

    • Estimating periodic signals

    Modelling Evolution¶

    • The simplest script
    • Performing a relative rate test
    • A test of the neutral theory
    • Allowing substitution model parameters to differ between branches
    • Using codon models
    • Use an empirical protein substitution model
    • Likelihood analysis of multiple loci
    • Simulate an alignment
    • Performing a parametric bootstrap
    • Perform a coevolutionary analysis on biological sequence alignments
    • Analysis of rate heterogeneity
    • Evaluate process heterogeneity using a Hidden Markov Model

    Phylogenetic Reconstruction¶

    • Calculate pairwise distances between sequences
    • Make a neighbor joining tree
    • Make a UPGMA cluster
    • Phylogenetic reconstruction by least squares

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