Biopython
Biopython is an open-source collection of non-commercial Python modules for computational biology and bioinformatics. It makes robust and well-tested code easily accessible to researchers. Python is an object-oriented programming language and is a suitable choice for automation of common tasks. The availability of reusable libraries saves development time and lets researchers focus on addressing scientific questions. Biopython is constantly updated and maintained by a large team of volunteers across the globe.
Key facts
- Software.name
- Biopython
- Software.logo
- Biopython logo.png
- Software.author
- Chapman B, Chang J
- Software.latest release version
- v1.87
- Software.programming language
- Python, C
- Software.platform
- Cross platform
- Software.genre
- Bioinformatics
- Software.license
- BSD 3-clause license
via Wikipedia infobox
Source code
The git repository at produces the Biopython website at using GitHub Pages (rendered using Jekyll, see for details). Almost all of the content is under the URL prefix /wiki/ because this was based on an automated conversion of the old MediaWiki website, using to turn all the changes in the MediaWiki XML export file into into markdown (using pandoc) as a git repository. The old MediaWiki usernames were manually mapped to GitHub accounts. About 20 accounts on the wiki (mostly single contributions) could not be identified, but the old username is still logged in the git commits. Note the website content under /DIST/ is hosted in a separate GitHub Pages project repository covering the Biopython releases and assorted documentation files.
~15 min read
Article
16 sectionsContents
- History
- Design
- Requirements
- Key features and examples
- Input and output
- Sequences
- Sequence annotation
- Accessing online databases
- Phylogeny
- Genome diagrams
- Macromolecular structure
- Population genetics
- Wrappers for command line tools
- See also
- References
- External links
Biopython is an open-source collection of non-commercial Python modules for computational biology and bioinformatics. It makes robust and well-tested code easily accessible to researchers. Python is an object-oriented programming language and is a suitable choice for automation of common tasks. The availability of reusable libraries saves development time and lets researchers focus on addressing scientific questions. Biopython is constantly updated and maintained by a large team of volunteers across the globe.
Biopython contains parsers for diverse bioinformatic sequence, alignment, and structure formats. Sequence formats include FASTA, FASTQ, GenBank, and EMBL. Alignment formats include Clustal, BLAST, PHYLIP, and NEXUS. Structural formats include the PDB, which contains the 3D atomic coordinates of the macromolecules. It has provisions to access information from biological databases like NCBI, Expasy, PBD, and BioSQL. This can be used in scripts or incorporated into their software. Biopython contains a standard sequence class, sequence alignment, and motif analysis tools. It also has clustering algorithms, a module for structural biology, and a module for phylogenetics analysis.