aakbar 0.5.1

Amino-Acid k-mer Phylogenetic Signature Tools

Amino-Acid k-mer tools for creating, searching, and analyzing phylogenetic signatures from genomes and from short reads of DNA.

Prerequisites

A 64-bit Python 3.4 or greater is required. 8 GB or more of memory is recommended.

The python dependencies of aakbar are: biopython, click>=5.0, click_plugins numpy, pandas, pyfaidx, and pyyaml. Running the examples also requires pyfastaq

If you don’t have a python installed that meets these requirements, I recommend getting Anaconda Python <https://www.continuum.io/downloads> on MacOSX and Windows for the smoothness of installation and for the packages that come pre-installed. Once Anaconda python is installed, you can get the dependencies like this on MacOSX:

export PATH=~/anaconda/bin:${PATH}    # you might want to put this in your .profile
conda install --channel https://conda.anaconda.org/IOOS click-plugins
conda install --channel https://conda.anaconda.org/bioconda pyfastaq

Installation

This package is tested under Linux and MacOS using Python 3.5 and is available from the PyPI:

pip install aakbar

If you wish to develop aakbar, download a release and in the top-level directory:

pip install --editable .

If you wish to have pip install directly from git, use this command:

pip install git+https://github.com/ncgr/aakbar.git#egg=proj

Basic Use

aakbar is implemented as a command-line program with subcommands. To list these subcommands:

aakbar --help

Documentation

• Readthedocs documentation

License

aakbar is distributed under a BSD License.