Triclosan tolerance is driven by a conserved mechanism in diverse Pseudomonas species

For help or any data requests, please contact Alex McFarland. email: alexandermcfarland2022@u.northwestern.edu

The repository for this project four folders with the data and R script used to analyze the data:

1. ani_anlysis
2. phylognetic_analysis
3. quality_assessments
4. susceptibility analysis

In order to run the analyses yourself, please do the following:

Download the data and script from the folder.

Unzip the data

Change the main_path variable to the folder containing the downloeaded data.

Run the analyses.

R was run version 4.0.2 on a x86_64-apple-darwin17.0 (64-bit) platform. These scripts were tested to work using R ersion 4.0.2 on MacOS (x86_64-apple-darwin17.0) (64-bit).

Please contact me if there are issues downlaoding certain libraries.

Additional info

The concatenated 34 gene marker tree is located in the phylogenetic_analysis with the filename RAxML_bipartitions.conctat34mlsa.

The data used to generate mauve whole genome anlignments are in the mauve_alignments folder.

All raw figures (not arranged/beautified in illustrator and used in the final version of the paper) are located in the figures folder.

FabV sequences detected in the 160 type strains, 30 study isolates, or 7,163 Pseudomonas genomes are located in the fabv_seqs_phylogeny folder.

The python code used to work with genomes, sequence data, islandviewer and iceberg submission, are loated in the python_scripts folder.