getphylo 0.0.2

a python package for automated generation of heuristic phylogenetic trees from genbank files

getphylo

a python package for automated generation of heuristic phylogenetic trees from genbank files

Description

WIP

Installation

Important: The following intructuons are for Linux and assume you have Python and pip installed already. For installation on different systems, please see the links provided for this individual dependences.

1. Installation of getphylo

Installation with PyPI

Coming soon!

Manual Installation

If you want to install getphylo manually, you can do so by cloning this repository.

git clone https://github.com/DrBoothTJ/getphylo cd getphylo python setup.py install

2. Installation of dependences

Important: Getphylo requires DIAMOND, MUSCLE and FastTree2 to be installed to work correctly. These must be installed manually. BioPython should be installed automatically. Below are instructions to install each dependency:

Installing DIAMOND

You can install DIAMOND with the following command:

sudo apt install diamond-aligner

Further instructions for installing DIAMOND can be found, here: https://github.com/bbuchfink/diamond/wiki/2.-Installation.

Installing MUSCLE

You can install MUSCLE with the following command:

WIP

Installing FastTree2

You can install FastTree2 with the following command:

sudo apt install fasttree

Further instructions for installing FastTree2 can be found, here: http://www.microbesonline.org/fasttree/.

Installing BioPython

If you installed getphylo using PyPI, BioPython should be installed automatically. If you installed getphylo manually, you will need to install BioPython yourself. This can be done using the command:

pip install biopython

Further instructions for installing FastTree2 can be found, here: https://biopython.org/wiki/Download.

Usage

This package has been designed to be as easy to run as possible. Simply navigate to a working directory containing .gbk files and input:

getphylo

This will run the software on default settings and output all alignments and trees.

There may be occasions where you need to change the default settings. A full list of options and flags can be viewed with:

getphylo -h

Below is a breif describtion of each flag.

Flags

WIP

Examples

See the ´example_data´ folder in this directory for three example trees produced by getphylo.

1. A phylogeny of bacterial genomes
2. A phylogeny of eukaryotic mitochondrial genomes
3. A phylogeny of a biosynthetic super cluster
4. A phylogeny of primate genomes