Python Med¶
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This page was migrated from the old MoinMoin-based wiki. Information may be outdated or no longer applicable. For current documentation, see python.org.
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
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
kPAL¶
kPAL is a [k]-mer [p]rofile [a]nalysis [l]ibrary. 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
License: MIT
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 2.7 and Python 3 (Python 3.1 and all later versions)
requires: -
License: BSD