This repository contains the packages used, commands issued, and raw files to generate figures 1A and 1B for the manuscript titled "Evolution of PqsE as a Pseudomonas aeruginosa-specific regulator of LuxR-type receptor regulation: Evolutionary insights from Pseudomonas and Burkholderia". The goal of this repository is to increase transparency and reproducibility.
All input files can be found in the Data folder. Commands issued to generate phylogenetic trees can be found in the following markdown files:
PqsE_HhqE_orthologue__shortlist_workflow.mdmarkdown file containing the commands issued to generate figure 1A.PqsE_HhqE_orthologue__workflow.mdmarkdown file containing the commands issued to generate figure 1B.
List of packages, versions used, citations, and relevant links.
TrimGalore v0.6.7 doi.org/10.5281/zenodo.7598955
MUSCLE v.3.8.1551 Edgar, R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research 32, 1792–1797 (2004). doi:10.1186/1471-2105-5-113
trimAL v.1.4.1 Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009). doi:10.1093/bioinformatics/btp348
IQ-TREE v1.6.12 Nguyen, L. T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies. Mol Biol Evol 32, 268–274 (2015). doi:10.1093/molbev/msu300
iTOL v.6.7.1 Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 49, W293–W296 (2021). doi:10.1093/nar/gkab301