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To use the scripts you will required the following programs:

• Amphora2
• Bioperl
• Python
• Ipython notebook
• Biopython
• Bioperl
• Bash
• R
• Phylobayes

You need to replace ~/Copy/proyecto by your folder direction i.e. /.

In your folder i.e. / you need to create data folder and inside processed/ raw folders i.e. mkdir /data/ processed raw

All processes were automated in Bash Script. In Bash folder you can run the scripts following this order:

1. Pilot
2. ./descarga_piloto.sh (Download genomes for NCBI).
3. ./rastreo_piloto.sh (Search genetic markers)
4. ./recorte_alineamiento.sh (alignment and trimmer of genetic markers)