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
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