Metadata-Version: 1.0
Name: nwalign
Version: 0.1.3
Summary: Needleman-Wunsch global sequence alignment
Home-page: http://bitbucket.org/brentp/biostuff/
Author: brentp
Author-email: bpederse@gmail.com
License: BSD
Description: 
        ------------------------------------------------------------------------------
        nwalign: fast `cython`_  - `Needleman-Wunsch`_ alignment
        ------------------------------------------------------------------------------
        
        .. _`Needleman-Wunsch`: http://en.wikipedia.org/wiki/Needleman-Wunsch_algorithm
        .. _`scoring matrix`: http://en.wikipedia.org/wiki/Substitution_matrix
        .. _`cython`: http://cython.org
        
        This module provides a python module and a command-line interface to do global-
        sequence alignment using the `Needleman-Wunsch` algorithm. It uses `cython`_
        and numpy for speed.
        
        Example Command-Line Usage
        ==========================
        
        
        the nwalign executable is installed to the PATH by setuptools::
        
        $ nwalign alphabet alpet
        alphabet
        alp---et
        
        specify an alignment `scoring matrix`_ ::
        
        $ nwalign --matrix /usr/share/ncbi/data/BLOSUM62 EEAEE EEEEG
        EEAEE-
        EE-EEG
        
        
        Usage as a python module
        ========================
        ::
        
        >>> import nwalign as nw
        >>> nw.global_align("CEELECANTH", "PELICAN", matrix='PAM250')
        ('CEELECANTH', '-PELICA--N')
        
        
        the matrix is specified as the full path to an `scoring matrix`_ as
        is distributed with the NCBI toolset.
        
Keywords: bioinformatics alignment needleman-wunsch
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Text Processing
