DefensiveDGR

Bash script DefensiveDGR.sh downloads the data required, performs the analyses, and draws figures. It works in Ubuntu 18.04.6 LTS. Figure 9 was created manually with clinker 0.0.21. If all the dependencies are installed simply type in terminal:

  bash DefensiveDGR.sh

and wait. The analyses were completed in seven days on our desktop computer

List of dependencies:

python 3.8.5

• numpy 1.20.3
• matplotlib 3.4.3
• upsetplot 0.5.0
• Biopython 1.78
• scipy 1.6.2
• pandas 1.3.2
• argparse 1.4.0

R 4.1.2

• data.table 1.14.0
• dplyr 1.0.6
• tidyr 1.1.3
• rhmmer 0.1.0

This programs should be installed system-wide:

• prodigal 2.6.3
• chips from EMBOSS:6.6.0.0
• hmmsearch from HMMER 3.3.2
• MMseqs2 635911ecf4ca5a2615e42931d7c0c04fe39a55cf
• psiblast 2.6.0+
• blastdbcmd: 2.6.0+
• muscle 3.8.31
• mafft 7.310