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Author Chih-Chung Chang and Chih-Jen Lin
URL http://www.csie.ntu.edu.tw/~cjlin/libsvm/
Description LIBSVM is an integrated software for support vector classification, regression and distribution estimation. It includes a python interface and excellent documentation about SVMs.
Name PyML
Author Asa Ben-Hur
URL http://pyml.sourceforge.net/
Description PyML is a flexible Python framework for using various classification methods including Support Vector Machines (SVM). It provides tools for model selection and feature selection.
Name PyMOL
Author Warren DeLano
URL http://www.pymol.org/
Description PyMOL is an open-source molecular modeling program written in the Python language. A number of Python scripts are available which link PyMOL to standard structure analysis programs.
Name GenomeDiagram (included in Biopython since release 1.50)
Author Leighton Pritchard
URL https://ics.hutton.ac.uk/software/tools/
Description A genomic and biological sequence schematic drawing package. Creates publication-quality genome schematics in several vector and bitmap formats.
Name Python Macromolecular Library (mmLib)
Author Jay Painter
URL http://pymmlib.sourceforge.net/
Description The Python Macromolecular Library (mmLib) is a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language. It is accessed via a layered, object-oriented application programming interface, and provides a range of useful software components for parsing mmCIF, PDB, and MTZ files, a library of atomic elements and monomers, an object-oriented data structure describing biological macromolecules, and an OpenGL molecular viewer.
Name pyzerg
Author Leighton Pritchard
URL https://pypi.python.org/pypi/PyZerg/0.1
Description A Python wrapper for the Zerg BLAST parser, a very fast BLAST parser library written in C.
Name Pycluster
Author Michiel de Hoon
URL https://pypi.python.org/pypi/Pycluster
Description This is a Python C extension module for clustering gene expression data. The exact same package is available as part of Biopython (see Bio.Cluster).
Name Dinu Gherman’s alignment code
Author Dinu Gherman
URL http://starship.python.net/crew/gherman/potpurri/align/
Description Code for pairwise sequence alignments.
Name Open Infrastructure for Outcomes (OIO)
Author Andrew P. Ho
URL http://www.TxOutcome.Org/
Description OIO is a free (as in GPL) web-based research and clinical data system that provides user-extensible plug-and-play components and data mining tools. We use it at Harbor-UCLA for health/treatment outcomes data. Forms/metadata can be exported+imported as XML and exchanged via the online OIO Library at www.TxOutcome.Org. It is written in Zope/Python and uses the PostgreSQL database backend. It has not been used to manage gene sequence/annotation data to my knowledge but it would be trivial to extend it for those functions.
Name Arne Mueller’s BLAST parser
Author Arne Mueller
URL http://www.sbg.bio.ic.ac.uk/~mueller/
Description A parser for BLAST and PSI-BLAST written in and for python.
Name PyPhy
Author Thomas Sicheritz-Ponten
URL http://www.cbs.dtu.dk/~thomas/pyphy/pyphy.html
Description PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial genomes. PyPhy consists of AutoTree which automatically generates phylogenetic trees for each amino acid sequence in a FASTA file, and Xphylome which generates and visualizes the Phylome Maps for a microbial genome.
Name Scripps Molecular Graphics Labs Python Software
Author Michel Sanner
URL http://mgltools.scripps.edu/
Description This site contains code dealing with structural bioinformatics and molecular visualization. This includes MolKit, which reads molecules from a number of file formats; PyBabel, which builds up molecular structures; MSLib, which wraps up a molecular surface calculation library; Python Molecular Viewer (PMV), which provides a complete viewer; AutoDockTools, which provides a GUI to set up ligand to protein docking experiments; and many more.
Name Konrad Hinsen’s Python Page - MMTK and ScientificPython
Author Konrad Hinsen
URL http://dirac.cnrs-orleans.fr/MMTK/
Description Contains the Molecular Modeling Toolkit (MMTK), an open source program library for molecular simulation applications. Additionally, Konrad has ScientificPython, which collects a number of modules that are useful in scientific computing, including code for statistics, basic geometry, etc.
Name Paul Magwene’s Python Page
Author Paul Magwene
URL https://github.com/pmagwene?tab=repositories
Description This collects Paul’s modules for doing different tasks (and also has links and a nice essay about why he likes python). A particularly interesting module is disipyl, which provides an object oriented interface to the Dislin plotting library.
Name snpFC
Author Ram Krishna Shrestha
URL https://github.com/TeamMacLean/snpFC
Description snpFC is a a tool for easy to filter VCF records with filter parameters and compare two or more VCF records for obtaining unique and common records.