biopython 1.86

Freely available tools for computational molecular biology.

Stars: 4904, Watchers: 4904, Forks: 1865, Open Issues: 576

The biopython/biopython repo was created 16 years ago and the last code push was 5 days ago.
The project is very popular with an impressive 4904 github stars!

How to Install biopython

You can install biopython using pip

pip install biopython

or add it to a project with poetry

poetry add biopython

Package Details

Author

The Biopython Contributors

License

None

Homepage

https://biopython.org/

PyPi:

https://pypi.org/project/biopython/

Documentation:

https://biopython.org/wiki/Documentation

GitHub Repo:

https://github.com/biopython/biopython

Classifiers

• Scientific/Engineering
• Scientific/Engineering/Bio-Informatics
• Software Development/Libraries/Python Modules

Related Packages

Errors

A list of common biopython errors.

Code Examples

Here are some biopython code examples and snippets.

GitHub Issues

The biopython package has 576 open issues on GitHub

• Feat: Add NetworkX adapter for PDB NeighborSearch results
• Add timeout support to NCBIWWW.qblast
• Fix residue depth subprocess : Modernize process execution in ResidueDepth using subprocess.run
• Fix Entrez.Parser.DataHandler URL security check continuity (related to #5109 and #5114)
• Correctly clean up files generated by the Phylo tutorial.
• Migrate to pyproject.toml
• bwl1289/fix/5137/undefined-symbols
• Fix Numpy 2.4 compatibility in PDB/vectors.py
• Missing libm linkage causes undefined symbol errors
• MMCif2Dict doesn't parse all keys in extremely large structures
• Incompatible with NumPy 2.4
• Added PERMISSIVE argument to MMCIFParser as in PDBParser.
• PDBParser is not thread-safe when used in ThreadPoolExecutor
• Added depreciation error to MMTFParser.get_structure_from_url since RCSB no longer serves MMTF
• make sure that polar_angle is initialized even if the radius is zero,…

See more issues on GitHub