Amino-Acid k-mer Phylogenetic Signature Tools
Project description
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
License
aakbar is distributed under a BSD License.
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