{ "info": { "author": "Maurits Dijkstra", "author_email": "mauritsdijkstra@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Environment :: Console", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU General Public License v2 (GPLv2)", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3.6" ], "description": "# PRALINE\n\nReimplementation of the PRALINE multiple sequence alignment program.\n\n# Features\n\n* Progressive multiple sequence alignment\n* Tree generation through hierarchical clustering and on-the-fly (PRALINE-style)\n* Profile-profile pairwise alignment\n* Affine and linear gap penalties supported; arbitrary gap penalties supported w/ reduced speed\n* Semi-global, global alignment for the MSA merge step\n* Local, global and semi-global preprofile generation\n* Improved preprofile sampling through PSI-BLAST search (requires local installation of NCBI BLAST+)\n* Nucleotide and amino acid alphabets supported out of the box\n* Easy to extend to with arbitrary alphabets (e.g. secondary sequence)\n* Packaged with common substitution matrices (BLOSUM), can be provided to the program.\n\n# Coming soon\n\n* HMM-like gap penalties per position\n* Heuristics to speed up tree building for large numbers of sequences\n* Better multithreading for improved scaling on many-core systems\n\n# Installing PRALINE\n\n## Requirements\n\n* Python 2.7 / Python 3.6 (earlier 3.x versions may also work, but have not been tested)\n* A C compiler (C99 support required)\n* NCBI BLAST+ (optional, for homology searching using PSI-BLAST)\n\n## Instructions\n\nYou can install PRALINE by cloning this repository and running (in a shell):\n\n`python setup.py install`\n\nPRALINE is also available on PyPI. 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