Tools for Computational Molecular Biology

 

The Biopython Project is a collection of freely available Python tools for computational molecular biology. The web site provides an online resource for modules, scripts, and web links for developers of Python-based software for life science research.

From the Tutorial and Cookbook on Biopython:

 

 

  • The ability to parse bioinformatics files into Python utilizable data structures
  • Code to deal with popular on-line bioinformatics
  • Interfaces to common bio-informatics programs
  • A standard sequence class that deals with sequences, ids on sequences, and sequence features.
  • Code to perform classification of data using k Nearest Neighbors, Naive Bayes or Support Vector Machines.
  • Code for dealing with alignments, including a standard way to create and deal with substitution matrices.
  • Code making it easy to split up parallelizable tasks into separate processes.
  • GUI-based programs to do basic sequence manipulations, translations, BLASTing, etc..
  • Integration with BioSQL, a sequence database schema also supported by the BioPerl and BioJava projects.

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