Python Tools for Computational Molecular Biology
Python Tools for Computational Molecular Biology
| Name | LIBSVM |
| 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. |