4. Advanced Usage Examples

This section contains examples used to demonstrate the utility and usage of getphylo.

For the inputs, alignments and trees relevant to each analysis, visit getphylo's benchmarking repository.

Example 1: Basic Usage

Example 1 illustrates the basic usage of getphylo. It is a good example to emulate if you want to check getphylo is installed correctly and working as intended.

First, clone the benchmarking repository and copy the example data to a new working directory:

git clone git@github.com:drboothtj/getphylo_benchmarking.git

mkdir example

cp getphylo getphylo_benchmarking/case_studies/case_study_1/*.gb example/

You can now delete the benchmarking repository. Always use caution when using rm -rf. You have been warned!

rm -rf getphylo_benchmarking

Now run getphylo:

getphylo -g ‘example/*.gb’ -o example/output -l INFO -cp 8

The run should be complete in less than 1 minute. If it has worked correctly, we should have a completed tree.

ls example/output/tree

You can now use your preferred visualization tool to examine the resulting tree.

Example 2: Starting from Proteomes (e.g. you do not have access to GenBank files)

WIP

Example 3: Analyzing Gene Clusters

Introduction

A powerful use for getphylo is to analyse gene clusters. However, it is very easy to misinterpret the results. It is particularly important when analysing gene clusters to understand your input and getphylo's output. In this example, I will detail my workflow for using getphylo to analyse the evolution of biosynthetic gene clusters (BGCs). We will use the example of the mosaic BGC for Svetamycin published here. To follow along with this tutorial, you will also need to install cblaster.

Preparing your input

WIP