|Travis| |PyPI| |Landscape| |Codecov|
alfpy
=====
alfpy is a bionformatics Python package that provides alignment-free framework
to compare biological sequences (DNA/RNA/protein) and infers their
phylogenetic relationships.
alfpy also contains Python scripts with user-friendly command-line interfaces
that let you compare unaligned FASTA sequences with more than 40 distance methods.
Latest source code
------------------
The official source code repository is at: https://github.com/aziele/alfpy
Web sites
---------
alfpy is also available as a web app: http://www.combio.pl/alfree
Requirements
============
1. Python (https://www.python.org/) version 2.7 or >= 3.3
2. NumPy (http://www.numpy.org/).
Installation
============
Option 1: Get the latest official version
-----------------------------------------
Install the latest official version with `pip <https://pip.pypa.io/en/stable/installing/>`_
::
sudo pip install alfpy
If you are not allowed to use `sudo`, install alfpy as user::
sudo pip install --user alfpy
Option 2: Get the latest development version
--------------------------------------------
Get it using this shell command, which requires Git::
git clone https://github.com/aziele/alfpy.git
If you don't feel like using git, just download the package manually as a `gzipped tarball <https://github.com/aziele/alfpy/archive/master.zip/>`_.
Unpack the zip package, go to the directory and run the installation::
cd alfpy
python setup.py install
or::
python setup.py install --user
Alfpy usage
===========
The examples of using Alfpy are available at: http://www.combio.pl/alfree/download/.
Testing
=======
To run tests, go to the alfpy source code directory and type::
python -m unittest discover
If you want to test a specific file (e.g. ``test_word_distance.py``), type::
python -m unittest tests.test_word_distance
Contact
=======
Drop us any feedback at: bioinfo@amu.edu.pl or on twitter `@a_zielezinski <https://twitter.com/a_zielezinski>`_.
License
=======
alfpy is under the MIT license; see ``LICENSE.txt``. Distribution,
modification and redistribution, incorporation into other software,
and pretty much everything else is allowed.
.. |Travis| image:: https://travis-ci.org/aziele/alfpy.svg?branch=master
:target: https://travis-ci.org/aziele/alfpy
.. |PyPI| image:: https://img.shields.io/pypi/v/alfpy.svg?branch=master
:target: https://pypi.python.org/pypi/alfpy
.. |Landscape| image:: https://landscape.io/github/aziele/alfpy/master/landscape.svg?style=flat
:target: https://landscape.io/github/aziele/alfpy/master
:alt: Code Health
.. |Codecov| image:: https://codecov.io/gh/aziele/alfpy/branch/master/graph/badge.svg
:target: https://codecov.io/gh/aziele/alfpy
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