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(>=2.0.14.152), MUSCLE(>=3.8.1551) and FastTree2(>=2.1.11) 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

Example outputs and benchmarking data can be found in the getphylo benchmarking repository. The example data includes:

1. A phylogeny of bacterial genomes,
2. A phylogeny of a biosynthetic gene cluster,
3. A phylogeny of primate genomes,
4. A phylogeny of Eurotiomycete fungi.

Citation

If you use getphylo, please cite:

Booth, T. J., Shaw, S., & Weber, T. (2023). getphylo: rapid and automatic generation of multi-locus phylogenetic trees. BioRxiv, 2023.07.26.550493.

DOI: https://doi.org/10.1101/2023.07.26.550493

Patch Notes

Version 0

• 0.1.0
  • beta version initial release
• 0.1.1
  • added support for MUSCLE5
• 0.1.2
  • now raises an error if translations are present but empty
  • error messages from the extract module are now more informative
  • fixed a fatal issue with --build-all
• 0.2.0
  • now supports iqtree using the --method parameter
• 0.2.1
  • now able to provide custom paths for binary dependencies
  • parser now has argument groups and is more readable
  • file exists error message more informative
• 0.2.2
  • added error message when users attempt to input directory instead of a search string
• 0.3.0
  • now supports modifying blastp thresholds, including parameters for identity and coverage
  • fixed typos in parser
  • fixed crashing when provided with directories with spaces in the names
• 0.3.1
  • fixed issue with the query and subject cover in diamond
• 0.3.2
  • added version info to setup.py and README for none-python dependencies
  • now raises error if the user provides too few input files
  • now raises an error if an invalid phylogentic method is provided (e.g. not fasttree or iqtree)