Bioinformatic analyses performed for the research paper:
Javier DelaFuente, Laura Toribio-Celestino, Alfonso Santos-Lopez, Ricardo León-Sampedro, Aida Alonso-del Valle, Coloma Costas, Lun Cui, Jerónimo Rodríguez-Beltrán, David Bikard, Rafael Cantón and Álvaro San Millán. Within-patient evolution of plasmid-mediated antimicrobial resistance. Nat Ecol Evol (2022). https://doi.org/10.1038/s41559-022-01908-7
Workflow and analysis criteria are described in within_patient_evolution.md
Additional files necessary for analysis are provided: ltrA.fasta and pOXA-48_K8.gb