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{| {{table}} width="100%"
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| Name          || MDMR
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|-
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| Author        || Matthew Zapala, Ondrej Libiger and Nicholas Schork
 +
|-
 +
| URL          || http://polymorphism.scripps.edu/~cabney/MatrixRegression.py.txt
 +
|-
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| Description  || MDMR is a Multivariate Distance Matrix Regression program that performs linear regression on a distance matrix of data and associates multiple independent variables to that matrix. 
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|}
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{| {{table}} width="100%"
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| Name          || PYRAXML2
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|-
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| Author        || Frank Kauff
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|-
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| URL          || http://www.lutzonilab.net/downloads/index.shtml
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|-
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| Description  || A python wrapper for RAxML-VI-HPC.  This is a python script that reads nexus data files and prepares the necessary input files and command line options for [http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm RAxML].
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|}
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{| {{table}} width="100%"
 
| Name          || LIBSVM
 
| Name          || LIBSVM
 
|-
 
|-
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{| {{table}} width="100%"
 
| Name          || PyML
 
| Name          || PyML
 
|-
 
|-
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| Name          || PyMOL
 
| Name          || PyMOL
 
|-
 
|-
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| Name          || GenomeDiagram
 
| Name          || GenomeDiagram
 
|-
 
|-
 
| Author        || Leighton Pritchard
 
| Author        || Leighton Pritchard
 
|-
 
|-
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| URL            || http://bioinf.scri.sari.ac.uk/lp/genomediagram.shtml
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| URL            || http://bioinf.scri.ac.uk/lp/programs.php
 
|-
 
|-
 
| Description    || A genomic and biological sequence schematic drawing package. Creates publication-quality genome schematics in several vector and bitmap formats.
 
| Description    || A genomic and biological sequence schematic drawing package. Creates publication-quality genome schematics in several vector and bitmap formats.
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| Name          || Python Macromolecular Library (mmLib)
 
| Name          || Python Macromolecular Library (mmLib)
 
|-
 
|-
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| Name pyzerg
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| Name           || pyzerg
 
|-
 
|-
 
| Author        || Leighton Pritchard
 
| Author        || Leighton Pritchard
 
|-
 
|-
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| URL            || http://bioinf.scri.sari.ac.uk/lp/pyzerg.shtml
+
| URL            || http://bioinf.scri.ac.uk/lp/programs.html
 
|-
 
|-
 
| Description    || A Python wrapper for the Zerg BLAST parser, a very fast BLAST parser library written in C.
 
| Description    || A Python wrapper for the Zerg BLAST parser, a very fast BLAST parser library written in C.
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| Name          || Pise Biopython client
 
| Name          || Pise Biopython client
 
|-
 
|-
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| Name Pycluster
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| Name           || Pycluster
 
|-
 
|-
 
| Author        || Michiel de Hoon
 
| Author        || Michiel de Hoon
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| Name          || UPDB
 
| Name          || UPDB
 
|-
 
|-
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| Name          || Dinu Gherman's alignment code
 
| Name          || Dinu Gherman's alignment code
 
|-
 
|-
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| Name          || Open Infrastructure for Outcomes (OIO)
 
| Name          || Open Infrastructure for Outcomes (OIO)
 
|-
 
|-
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| Name          || Arne Mueller's BLAST parser
 
| Name          || Arne Mueller's BLAST parser
 
|-
 
|-
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| Name          || The Nilges group's python scripts
 
| Name          || The Nilges group's python scripts
 
|-
 
|-
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| Name          || PySAT
 
| Name          || PySAT
 
|-
 
|-
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| Name          || PyPhy
 
| Name          || PyPhy
 
|-
 
|-
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| Name          || Scripps Molecular Graphics Labs Python Software
 
| Name          || Scripps Molecular Graphics Labs Python Software
 
|-
 
|-
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| Name          || Konrad Hinsen's Python Page
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| Name          || Konrad Hinsen's Python Page - MMTK and ScientificPython
 
|-
 
|-
 
| Author        || Konrad Hinsen
 
| Author        || Konrad Hinsen
 
|-
 
|-
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| URL            || http://starship.python.net/crew/hinsen/
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| URL            || http://dirac.cnrs-orleans.fr/MMTK/ and http://dirac.cnrs-orleans.fr/ScientificPython/
 
|-
 
|-
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| Description    || Contains the Molecular Modeling Toolkit, 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.
+
| 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.
 
|}
 
|}
  
  
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{| {{table}} width="100%"
 
| Name          || Paul Magwene's Python Page
 
| Name          || Paul Magwene's Python Page
 
|-
 
|-
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| Name          || Noah Hoffman's Python Page
 
| Name          || Noah Hoffman's Python Page
 
|-
 
|-
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|-
 
|-
 
| Description    || A collection of python modules and scripts originally intended to process large collections of HIV sequences. Now contains general utilities for sequence analysis, manipulation, classification, and formatting. Plus other useful stuff.
 
| Description    || A collection of python modules and scripts originally intended to process large collections of HIV sequences. Now contains general utilities for sequence analysis, manipulation, classification, and formatting. Plus other useful stuff.
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|}
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{| {{table}} width="100%"
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| Name          || Vienna RNA package
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|-
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| Author        || Ivo Hofacker, Institut für theoretische Chemie, University of Vienna, Austria
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|-
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| URL          || http://www.tbi.univie.ac.at/RNA/
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|-
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| Description  || This is a package for RNA secondary structure prediction and comparison.  While it was not specifically written for Python, you can get the Python wrappers for it using the SWIG file that is included with the software package.  The easiest way is to first compile the Vienna RNA package as described in its documentation (you don't need to actually install it).  Then, run "swig -python RNA.i" in the ViennaRNA-1.8.4/Perl directory. This will create a new RNA_wrap.c specifically for Python, as well as RNA.py.
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Next, you should compile RNA_wrap.c. You can use this setup.py script:
 +
<python>
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#!/usr/bin/env python
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from distutils.core import setup, Extension
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import os
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import sys
 +
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old_filename = os.path.join("Perl", "RNA.py")
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new_filename = os.path.join("Perl", "__init__.py")
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if os.path.exists(old_filename):
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    os.rename(old_filename, new_filename)
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extra_link_args = []
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if sys.platform != 'darwin':
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    extra_link_args.append('-s')
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extension = Extension("_RNA",
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                      ["Perl/RNA_wrap.c"],
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                      libraries=['RNA'],
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                      library_dirs=['lib'],
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                      extra_link_args=extra_link_args
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                      )
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setup(name="RNA",
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      version="1.8.4",
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      description="Vienna RNA",
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      author="Ivo Hofacker, Institute for Theoretical Chemistry, University of Vienna",
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      url="http://www.tbi.univie.ac.at/RNA/",
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      package_dir = {'RNA':'Perl'},
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      packages = ['RNA'],
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      ext_modules=[extension],
 +
      )
 +
</python>
 +
 +
Put this setup.py in the ViennaRNA-1.8.4 directory, and run "python setup.py build; python setup.py install" as usual.
 +
 +
To try the package, use
 +
<python>
 +
>>> import RNA
 +
>>> RNA.fold('CCCCCAAAGGGGG')
 +
['(((((...)))))', -7.5]
 +
>>>
 +
</python>
 +
|}
 +
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{| {{table}} width="100%"
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| Name          || SeqMagick
 +
|-
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| Author        || Erick Matsen, Connor McCoy, Brian Hodges, Aaron Gallagher
 +
|-
 +
| URL          || http://fhcrc.github.com/seqmagick
 +
|-
 +
| Description  || SeqMagick is a simple tool for querying and modifying, and converting sequence files from the command line.
 
|}
 
|}

Latest revision as of 18:32, 8 July 2011

Name MDMR
Author Matthew Zapala, Ondrej Libiger and Nicholas Schork
URL http://polymorphism.scripps.edu/~cabney/MatrixRegression.py.txt
Description MDMR is a Multivariate Distance Matrix Regression program that performs linear regression on a distance matrix of data and associates multiple independent variables to that matrix.


Name PYRAXML2
Author Frank Kauff
URL http://www.lutzonilab.net/downloads/index.shtml
Description A python wrapper for RAxML-VI-HPC. This is a python script that reads nexus data files and prepares the necessary input files and command line options for RAxML.


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://cmgm.stanford.edu/~asab/pyml/pyml.html
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://pymol.sourceforge.net/
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
Author Leighton Pritchard
URL http://bioinf.scri.ac.uk/lp/programs.php
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 http://bioinf.scri.ac.uk/lp/programs.html
Description A Python wrapper for the Zerg BLAST parser, a very fast BLAST parser library written in C.


Name Pise Biopython client
Author Catherine Letondal
URL http://www.pasteur.fr/recherche/unites/sis/Pise/#pisepython
Description This package runs remote analyses on a Pise Web server. There are currently about 300 programs available, including EMBOSS and Phylip, several phylogeny, sequence comparison, 3D structure, pattern discovery, gene prediction and DNA, protein or RNA analyses programs. The package automatically chain programs to extract results as file, string or filehandle for Biopython modules. It also accepts Biopython sequences and alignment class as input data.


Name Pycluster
Author Michiel de Hoon
URL http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/
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 UPDB
Author Andrew Dalke
URL ftp://ftp.ks.uiuc.edu/pub/group/dalke/UPDB-0.5.tar.gz
Description A Python script that reads the PDB format documentation and generates code for a given language to parse and/or generate column delimited record format used by the PDB.


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 The Nilges group's python scripts
Author Michael Nilges and the structural bioinformatics research group
URL http://www.pasteur.fr/recherche/unites/Binfs/
Description Python code for structural bioinformatics and data transformation.


Name PySAT
Author Chenna Ramu
URL http://www.embl-heidelberg.de/~chenna/PySAT/
Description Python Sequence Analysis Tools consists of modules to parse and iterate through various flat file databases (EMBL, GENBANK, SWISSPROT, PDBFINDER, ENZYME etc.) and does a few other things.


Name PyPhy
Author Thomas Sicheritz-Ponten
URL http://www.cbs.dtu.dk/staff/thomas/pyphy/
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://www.scripps.edu/~sanner/python/index.html
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/ and http://dirac.cnrs-orleans.fr/ScientificPython/
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 http://kim.bio.upenn.edu/~pmagwene/programming.html
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 Noah Hoffman's Python Page
Author Noah Hoffman and Wolfgang Resch
URL http://www.unc.edu/~nghoffma/software.html
Description A collection of python modules and scripts originally intended to process large collections of HIV sequences. Now contains general utilities for sequence analysis, manipulation, classification, and formatting. Plus other useful stuff.


Name Vienna RNA package
Author Ivo Hofacker, Institut für theoretische Chemie, University of Vienna, Austria
URL http://www.tbi.univie.ac.at/RNA/
Description This is a package for RNA secondary structure prediction and comparison. While it was not specifically written for Python, you can get the Python wrappers for it using the SWIG file that is included with the software package. The easiest way is to first compile the Vienna RNA package as described in its documentation (you don't need to actually install it). Then, run "swig -python RNA.i" in the ViennaRNA-1.8.4/Perl directory. This will create a new RNA_wrap.c specifically for Python, as well as RNA.py.

Next, you should compile RNA_wrap.c. You can use this setup.py script: 

#!/usr/bin/env python
 
from distutils.core import setup, Extension
import os
import sys
 
old_filename = os.path.join("Perl", "RNA.py")
new_filename = os.path.join("Perl", "__init__.py")
if os.path.exists(old_filename):
    os.rename(old_filename, new_filename)
 
extra_link_args = []
if sys.platform != 'darwin':
    extra_link_args.append('-s')
 
extension = Extension("_RNA",
                      ["Perl/RNA_wrap.c"],
                      libraries=['RNA'],
                      library_dirs=['lib'],
                      extra_link_args=extra_link_args
                      )
 
setup(name="RNA",
      version="1.8.4",
      description="Vienna RNA",
      author="Ivo Hofacker, Institute for Theoretical Chemistry, University of Vienna",
      url="http://www.tbi.univie.ac.at/RNA/",
      package_dir = {'RNA':'Perl'},
      packages = ['RNA'],
      ext_modules=[extension],
      )

Put this setup.py in the ViennaRNA-1.8.4 directory, and run "python setup.py build; python setup.py install" as usual.

To try the package, use 

>>> import RNA
>>> RNA.fold('CCCCCAAAGGGGG')
['(((((...)))))', -7.5]
>>>
Name SeqMagick
Author Erick Matsen, Connor McCoy, Brian Hodges, Aaron Gallagher
URL http://fhcrc.github.com/seqmagick
Description SeqMagick is a simple tool for querying and modifying, and converting sequence files from the command line.
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