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      • Previous: Useful Utilities
      • Next: Translating DNA into protein

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Usage Examples¶

Data manipulation¶

  • Translating DNA into protein
  • Advanced sequence handling
  • Complete version of manipulating sequence annotations
  • Getting the reverse complement
  • Map protein alignment gaps to DNA alignment gaps
  • Data Manipulation using Table
  • 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
  • Making a phylogenetic tree from a protein sequence alignment
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