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

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 (Cock et al., 2009) and/or one of the other listed papers:

  1. Cock PA, Antao T, Chang JT, Bradman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B and de Hoon MJL (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25, 1422-1423

    This application note covers the whole of Biopython

  2. Chapman BA and Chang JT (2000). Biopython: Python tools for computational biology. ACM SIGBIO Newsletter, 20, 15-19

    HTML | PDF

    This served as the official project announcement

  3. Hamelryck T and Manderick B (2003) PDB file parser and structure class implemented in Python. Bioinformatics, 22, 2308-2310

    The Bio.PDB module is described here

  4. de Hoon MJ, Imoto S, Nolan J and Miyano S (2004) Open source clustering software. Bioinformatics, 20, 1454-1453

    The Bio.Cluster module is described here

  5. Pritchard L, White JA, Birch PR and Toth IK (2006) GenomeDiagram: a Python package for the visualization of large-scale genomic data. Bioinformatics, 22, 616-617

    This describes GenomeDiagram, which has now been integrated into Biopython

  6. Cock PJ, Fields CJ, Goto N, Heuer ML and Rice PM (2009) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res., 38, 1767-1771

    This describes the FASTQ file format as supported in Biopython, BioPerl, BioRuby, BioJava and EMBOSS

  7. Talevich E, Invergo BM, Cock PJ and Chapman BA (2012) Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. BMC Bioinformatics, 13, 209

    This describes the Bio.Phylo and Bio.Phylo.PAML modules


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