Alignment-free package to compare DNA/RNA/protein sequences (bioinformatics).
Project description
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
Python (https://www.python.org/) version 2.7 or >= 3.3
NumPy (http://www.numpy.org/).
Installation
Option 1: Get the latest official version
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
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.
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.
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.
