= 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 [[http://wiki.debian.org/DebianMed|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|NumPy]]

 * License: [[http://www.biopython.org/DIST/LICENSE|Biopython license]]

 * [[http://biopython.org/wiki/Biopython|Biopython wiki]] [[https://pypi.python.org/pypi/biopython|Biopython at PyPI]]

 * Linux packages: [[https://packages.debian.org/search?searchon=sourcenames&keywords=python-biopython|python-biopython Debian packages]] [[http://packages.ubuntu.com/search?suite=default&section=all&arch=any&keywords=biopython&searchon=sourcenames|python-biopython Ubuntu packages]] [[https://apps.fedoraproject.org/packages/python-biopython|python-biopython Fedora package]] [[https://www.archlinux.org/packages/?q=biopython|python-biopython Archlinux packages]]

== pysam ==
pysam is a Python wrapper package around [[http://www.htslib.org/|Samtools]], a suite of programs for reading and manipulating high-throughput sequencing data.

 * compatible with Python 2 and 3

 * requires: [[http://cython.org/|Cython]]

 * License: MIT

 * [[https://github.com/pysam-developers/pysam|pysam on github]] [[http://pysam.readthedocs.org|pysam documentation]]

== 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

 * requires: NumPy, [[http://www.h5py.org|h5py]], [[#Biopython|Biopython]]

 * License: MIT

 * [[https://pypi.python.org/pypi/kPAL|kPAL at PyPI]] [[http://kpal.readthedocs.org|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 2.7 and Python 3 (Python 3.1 and all later versions)

 * requires: -

 * License: BSD

 * [[https://pypi.python.org/pypi/DendroPy|DendroPy at PyPI]] [[http://dendropy.readthedocs.org|DendroPy documentation]]


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CategoryPythonInScience