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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

  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

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.

Release History

Release History

This version
History Node

1.0.5

History Node

1.0.4

Download Files

Download Files

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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
alfpy-1.0.5.tar.gz (62.0 kB) Copy SHA256 Checksum SHA256 Source Jan 21, 2017

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