a python package for automated generation of heuristic phylogenetic trees from genbank files
Project description
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
.
- A phylogeny of bacterial genomes
- A phylogeny of eukaryotic mitochondrial genomes
- A phylogeny of a biosynthetic super cluster
- A phylogeny of primate genomes
Project details
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