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.

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