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        "author": "Antonio Ben\u00edtez-Hidalgo, Antonio J. Nebro",
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            "Development Status :: 3 - Alpha",
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            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 3.6",
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        "description": "<p align=\"center\">\n  <br/>\n  <img src=resources/pymsa.png alt=\"pyMSA\">\n  <br/>\n</p>\n\n# Scoring Multiple Sequence Alignments with Python\n[![Build Status](https://img.shields.io/travis/benhid/pyMSA.svg?style=flat-square)](https://travis-ci.org/benhid/pyMSA)\n[![PyPI License](https://img.shields.io/pypi/l/pyMSA.svg?style=flat-square)]()\n[![PyPI Python version](https://img.shields.io/pypi/pyversions/pyMSA.svg?style=flat-square)]()\n\npyMSA is an open source software tool aimed at providing a number of scores for\nmultiple sequence alignment (MSA) problems.\n\n## Features\nThe scores that are currently available are:\n* Sum of pairs,\n* Star,\n* Minimum entropy,\n* Percentage of non-gaps,\n* Percentage of totally conserved columns *and*\n* STRIKE (**S**ingle s**TR**ucture **I**nduced **E**valuation).\n\n## Downloading\nTo download PyMSA just clone the Git repository hosted in GitHub:\n```bash\n$ git clone https://github.com/benhid/pyMSA.git\n$ python setup.py install\n```\n\nAlternatively, you can install it with `pip`:\n```bash\n$ pip install pyMSA\n```\n\n### STRIKE score\nFor computing the [STRIKE](http://www.tcoffee.org/Projects/strike/) score, \nthe tool (v1.2) must be installed on the `usr/local/bin` folder.\n\n*e.g.* After compiling run:\n\n```bash\n$ sudo cp bin/strike /usr/local/bin\n```\n\n### Substitution matrices\n\npyMSA has only two available substitution matrices: *PAM250*  and *Blosum62*.\n\nOther substitution matrices can be used by reading a matrix [file](ftp://ftp.ncbi.nih.gov/blast/matrices/) with `read_matrix_from_file()` (from the `pymsa.util.substitution_matrix` module). `FileMatrix` implements this method by default:\n\n```python\nfrom pymsa.core.substitution_matrix import PAM250, Blosum62, FileMatrix\n\npam250 = PAM250()\nblosum62 = Blosum62()\npam380 = FileMatrix('PAM380.txt')\n```\n\n## Usage\nAn example of running all the included scores is located in the [`example`](example/) folder.\n\n## Authors\n### Active development team\n* Antonio Ben\u00edtez-Hidalgo <antonio.b@uma.es>\n* Antonio J. Nebro <antonio@lcc.uma.es>\n\n## License\nThis project is licensed under the terms of the MIT - see the [LICENSE](LICENSE) file for details.\n\n\n",
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