getphylo 0.1.0

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

getphylo: GEnbank To PHYLOgeny

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

Description

getphylo was designed to automatically build multi-locus phylogenetic trees from GenBank files. The workflow consists of the following steps: i) extract protein coding sequences; ii) screen for suitable markers; iii) align individual marker sequences and create a combined alignment; and iv) produce a tree from the combined alignment. Please see the 'parameters' section below for a full list of parameters.

Installation

The easiest way to install getphylo is using the command:

pip install getphylo

This will fetch and install the latest version from: https://pypi.org/project/getphylo/

For full installation instructions, please see the getphylo wiki.

Important: getphylo requires DIAMOND, MUSCLE and FastTree2 to be installed to work correctly. These must be installed manually. Further instructions are availiable on the wiki.

Quick-start

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 with default settings.

A full list of options and flags can be viewed with:

getphylo -h

A full list of parameters and further usage examples are availiable on the wiki.

Example Analysis and Datasets

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