Codebase

This repository contains the codebase used in the manuscript:

Perez-Quintero, Rodriguez-R, Cuesta-Morrondo, Hakalová, Betancurt-Anzola, Camelo Valera, Chica Cardenas, Matiz-Céron, Jacobs, Roman-Reyna, Reyes Muñoz, Bernal Giraldo, Koebnik. Comparative genomics of African cotton pathogens identifies conserved and variable TAL effectors in Xanthomonas citri pv. malvacearum

Required software

The following Software and their prerequisites are necessary:

  • MiGA
  • MMSeqs2
  • Phylophlan

Additionally, some scripts are prepared for the SLURM scheduler, but can be easily adapted for direct BASH execution