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Last edited by Mélanie HENNART

Execution of Jolytree via by the option --tree (see https://gitlab.pasteur.fr/GIPhy/JolyTree)

     JolyTree.sh -i $dirIn -b $dirOut -t $threads

Execution of integron finder version 2 --integron (see https://github.com/gem-pasteur/Integron_Finder)

     integron_finder --cpu $threads --outdir $dirOut --gbk --func-annot --mute $genome

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