PythonMed

This page attempts to collect all the Python packages associated with medicine, pre-clinical research, life science and bioinformatics for the community. Its modelled along the Debian Med project

Biopython

Biopython facilitates the use of Python for bioinformatics through high-quality, reusable modules and classes. Biopython features include parsers for various Bioinformatics file formats (BLAST, Clustalw, FASTA, Genbank,...), access to online services (NCBI, Expasy,...), interfaces to common and not-so-common programs (Clustalw, DSSP, MSMS...), a standard sequence class, various clustering modules, a KD tree data structure, etc.

• compatible with Python 2 and 3

• requires: NumPy

• License: Biopython license

• Biopython wiki Biopython at PyPI

• Linux packages: python-biopython Debian packages python-biopython Ubuntu packages python-biopython Fedora package python-biopython Archlinux packages

pysam

pysam is a Python wrapper package around Samtools, a suite of programs for reading and manipulating high-throughput sequencing data.

• compatible with Python 2 and 3

• requires: Cython

• License: MIT

• pysam on github pysam documentation

kPAL

kPAL is a k-mer profile analysis library. It can be used to count k-mers and to analyze and compare k-mer distributions in DNA sequences, which is itself useful, e.g., in quality control of DNA sequencing data. The package can be used as a command line tool or as a Python library.

• compatible with Python 2 and 3

• requires: NumPy, h5py, Biopython

• License: MIT

• kPAL at PyPI kPAL documentation

DendroPy

DendroPy is a package for phylogenetic computing. It supports a wide range of phylogenetic tree formats and can be used both as a phylogenetic library and for scripting.

• compatible with Python 2 (2.4+) only
• requires: -
• License: BSD

• DendroPy at PyPI DendroPy documentation

CategoryPythonInScience