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| 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]] | |
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| This page attempts to collect all the Python packages associated with medicine, pre-clinical research, life science and bio-informatics 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. |
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| == Bio Python == | * compatible with Python 2 and 3 |
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| * [[http://biopython.org/wiki/Biopython | BioPython wiki]] | * requires: [[NumPy|NumPy]] |
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| * Debian packages: [[http://packages.debian.org/unstable/python/python-biopython-sql | unstable release]] | * License: [[http://www.biopython.org/DIST/LICENSE|Biopython license]] |
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| * Ubuntu packages: [[http://packages.ubuntu.com/jaunty/python/python-biopython-sql | jaunty]] | * [[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§ion=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]] ---- CategoryPythonInScience |
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 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
- 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