Bacterial genomes differ in gene content since parts of their genome can be duplicated, lost, or picked up from the environment. The latter can be mediated by phages or dedicted DNA uptake mechanisms. This type of horizontal transfer complicates the phylogenetic analysis is bacteria. With the total number of genomes that are analyzed, the number of genes found in all strains (often referred to as the core genome) goes down, while the total number of distinct genes goes up (the pan-genome).
To install panX, type
git clone https://github.com/neherlab/pan-genome-analysis.git cd pan-genome-analysis git submodule update
on the command line. All other dependencies should be install already. This will now allow you to run the pipe-line, either on the test data provided or on the your own data.
The visualization is best installed on your own laptop. If you have
git install, the following series of commands should do the trick
git clone https://github.com/neherlab/pan-genome-visualization.git git submodule update --init npm install npm start