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phylobarcode

Leonardo de Oliveira Martins1
1. Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ, UK

Introduction

Phylobarcode is a tool to search and analyse long operons with phylogenetic signal.

It can search for potential long segments ('operons' or 'barcodes') which can serve as phylogenetic markers. It can then search for potential primers which can be used to amplify the operon. And it can be used to reconstruct the evolutionary history of the amplicons (unfinished).

This is an experimental software under active development, modules and functions may change without notice. Phylobarcode is not production-ready yet, please use at your own risk.

This software and the ideas behind it were supported by the COG-UK Early Career Funding Scheme (see also the announcement on linkedin)

Documentation

The documentation can be found in https://quadram-institute-bioscience.github.io/phylobarcode/

Installation

Requirements

  • conda
  • linux
  • python=3.9

The other requirements can be installed with conda. In particular parasail-python os not available yet for python 3.10

Generate a conda environment

This software depends on several other packages, installable through conda or pip. The suggested installation procedure is to create a conda environment (to take care of dependencies) and then installing the python package:

conda update -n base -c defaults conda # probably not needed, but some machines complained about it
conda env create -f environment.yml  
conda activate phylobarcode
python setup.py install # or "pip install ."

Since this software is still under development, these two commands are quite useful:

conda env update -f environment.yml # update conda evironment after changing dependencies
# installs in development mode (modifications to python files are live):
pip install -e .  # or python setup.py develop

License

SPDX-License-Identifier: GPL-3.0-or-later

Copyright (C) 2022-today Leonardo de Oliveira Martins

phylobarcode is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version (http://www.gnu.org/copyleft/gpl.html).

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