Python module

egglib-py is the Python version of eggLib. It contains a wrapper of the eggLib-cpp library generated using SWIG as well as additional functionalies and a number of pre-implemented applications that can be used directly through the executable script egglib.

The different parts of egglib-py are described in the following sections.

• Low-level binding of C++ library
  • Data holders
  • Conversion and parsing
  • Analysis of polymorphism
  • Coalescent simulator
  • Approximate Bayesian Computation
  • Random number generator
• Top-level Egglib components
  • Class Container
  • Class Align
  • Class SequenceItem
  • SSR class
  • TIGR class
  • GenBank class
  • Tree class
• tools
  • Specific data formats
  • Data analysis
  • Sequence manipulation tools
  • Sequence comparison
  • Tools not (directly) related to sequence data
• wrappers
  • Hudson’s coalescent simulator
  • NCBI BLAST tools
  • Sequence alignment
  • Tree building and analysis
  • Primer detection
• simul
  • Simulation function
  • Parameter holder class
  • Specifying mutation model using dedicated classes
• fitmodel
  • Utilities
  • Prior implementations
  • Demographic model implementations
  • Summary statistics implementations
• Utils module
• test