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New to Biopython? Check out the Getting Started page, or follow one of the links below.

  • Installation instructions cover the installation of Python itself, the Biopython dependencies, and Biopython itself.
    HTML | PDF
  • The Biopython Tutorial and Cookbook contains the bulk of Biopython documentation. It provides information to get you started with Biopython, in addition to specific documentation on a number of modules
    HTML | PDF
  • API documentation for Biopython modules is generated directly from source code comments using Epydoc.
  • Wiki documentation,
  • Documentation for the Biopython interfaces to BioSQL cover installing Python database adaptors and basic usage of BioSQL.
    HTML | PDF
  • Documentation for the cluster module in Biopython. This describes the underlying C library and the Python interface.
  • Cookbook-style documentation:
    • Cookbook documentation (on the wiki)
    • The Biopython Structural Bioinformatics FAQ (i.e. how to use the Bio.PDB module).
    • Working with restriction enzymes.

Documentation for Developers

Online Course Notes


We have a separate list of publications citing or using Biopython. If you use Biopython in a scientific publication, please cite the application note [1] and/or one of the other listed papers:

Error fetching PMID 19304878:
Error fetching PMID 14630660:
Error fetching PMID 14871861:
Error fetching PMID 16377612:
Error fetching PMID 20015970:
Error fetching PMID 22909249:
  1. Error fetching PMID 19304878: [CockEtAl2009]
    This application note covers the whole of Biopython

  2. Chapman BA and Chang JT. Biopython: Python tools for computational biology. ACM SIGBIO Newsletter 2000 Aug; 20, 15-19. HTML | PDF


    This served as the official project announcement.

  3. Error fetching PMID 14630660: [HamelryckAndManderick2003]
    The Bio.PDB module is described here.

  4. Error fetching PMID 14871861: [DeHoonEtAl2004]
    The Bio.Cluster module is described here.

  5. Error fetching PMID 16377612: [PritchardEtAl2006]
    This describes GenomeDiagram, which has now been integrated into Biopython.

  6. Error fetching PMID 20015970: [CockEtAl2009b]
    This describes the FASTQ file format as supported in Biopython, BioPerl, BioRuby, BioJava and EMBOSS

  7. Error fetching PMID 22909249: [TalevichEtAl2012]
    This describes the Bio.Phylo and Bio.Phylo.PAML modules.

All Medline abstracts: PubMed HubMed


  • BOSC 2013 presentation "Biopython Project Update"
    PDF | Flash version
  • BOSC 2012 presentation "Biopython Project Update"
    Flash version
  • BOSC 2011 presentation "Biopython Project Update"
    Flash version
  • BOSC 2010 presentation "Biopython Project Update"
    Flash version
  • July 2010 - EuroSciPy2010, Paris
  • February 2010 Biopython workshop at the University of Georgia
    PDF | Flash version
  • BOSC 2009 presentation "Biopython Project Update"
    PDF | Flash version
  • Scottish Bioinformatics Forum NextGenBug meeting June 2009 - Second generation sequence data and Biopython
  • Laptop session at "2009 Biología Computacional de Proteínas workshop" at Quilmes National University
    HTML (requires Crunchy to try the code online)
  • BOSC 2008 presentation "Biopython Project Update"
    PDF | Flash version
  • BOSC 2007 presentation "Biopython Project Update"
    PDF | Flash version
  • March 2004 presentation at Exelixis about Biopython. Includes code examples with Biopython libraries and Martel.
    PDF | tarball with LaTeX source
  • BOSC 2003 presentation about Biopython and using it for Laboratory Analysis Pipelines.
    PDF | tarball with LaTeX source
  • General talk about scripting with Biopython based example of a primer design program (old).
    PDF | tarball with LaTeX source
  • Talk about Python and Biopython with an emphasis on teaching the design goals of Biopython (old).
    PDF | tarball with LaTeX source

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