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.
The official source code repository is at: https://github.com/aziele/alfpy
alfpy is also available as a web app: http://www.combio.pl/alfree
- Python (https://www.python.org/) version 2.7 or >= 3.3
- NumPy (http://www.numpy.org/).
Install the latest official version with pip
sudo pip install alfpy
If you are not allowed to use sudo, install alfpy as user:
sudo pip install --user alfpy
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.
Unpack the zip package, go to the directory and run the installation:
cd alfpy python setup.py install
or:
python setup.py install --user
The examples of using Alfpy are available at: http://www.combio.pl/alfree/download/.
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
Drop us any feedback at: bioinfo@amu.edu.pl or on twitter @a_zielezinski.
alfpy is under the MIT license; see LICENSE.txt. Distribution,
modification and redistribution, incorporation into other software,
and pretty much everything else is allowed.