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Alignment-free package to compare DNA/RNA/protein sequences (bioinformatics).

Project Description


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:

Web sites

alfpy is also available as a web app:


  1. Python ( version 2.7 or >= 3.3
  2. NumPy (


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

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 install


python install --user

Alfpy usage

The examples of using Alfpy are available at:


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., type:

python -m unittest tests.test_word_distance


Drop us any feedback at: 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.

Release History

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Source None Mar 13, 2018

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