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 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.


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


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.


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.


PythonMed (last edited 2015-01-13 10:01:10 by WolfgangMaier)

Unable to edit the page? See the FrontPage for instructions.