Description:

alfpy 1.0.6

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.

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

Share

• Share on Facebook
• Share on Twitter