Metadata-Version: 2.1
Name: praline-aln
Version: 1.1.0
Summary: PRALINE sequence alignment toolkit
Home-page: https://github.com/ibivu/PRALINE/
Author: Maurits Dijkstra
Author-email: mauritsdijkstra@gmail.com
License: GPLv2
Description: # PRALINE
        
        Reimplementation of the PRALINE multiple sequence alignment program.
        
        # Features
        
        * Progressive multiple sequence alignment
        * Tree generation through hierarchical clustering and on-the-fly (PRALINE-style)
        * Profile-profile pairwise alignment
        * Affine and linear gap penalties supported; arbitrary gap penalties supported w/ reduced speed
        * Semi-global, global alignment for the MSA merge step
        * Local, global and semi-global preprofile generation
        * Improved preprofile sampling through PSI-BLAST search (requires local installation of NCBI BLAST+)
        * Nucleotide and amino acid alphabets supported out of the box
        * Easy to extend to with arbitrary alphabets (e.g. secondary sequence)
        * Packaged with common substitution matrices (BLOSUM), can be provided to the program.
        
        # Coming soon
        
        * HMM-like gap penalties per position
        * Heuristics to speed up tree building for large numbers of sequences
        * Better multithreading for improved scaling on many-core systems
        
        # Installing PRALINE
        
        ## Requirements
        
        * Python 2.7 / Python 3.6 (earlier 3.x versions may also work, but have not been tested)
        * A C compiler (C99 support required)
        * NCBI BLAST+ (optional, for homology searching using PSI-BLAST)
        
        ## Instructions
        
        You can install PRALINE by cloning this repository and running (in a shell):
        
        `python setup.py install`
        
        PRALINE is also available on PyPI. You can install it with the following command:
        
        `pip install praline`
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.6
Requires-Python: >=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.2.*,!=3.3.*,!=3.4.*
Description-Content-Type: text/markdown
