a python package for automated generation of heuristic phylogenetic trees from genbank files
Project description
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
.
- 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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