Good day @mattbull,
I have created a core genome with roary and am now interested in running roary plots, using the command, roary_plots.py name_of_your_newick_tree_file.tre gene_presence_absence.csv. I am following the protocol from Andrew page (http://sanger-pathogens.github.io/Roary/ ) however it appears some of the dependencies needed to run roary plots aren’t installed by default. Please, can you help?
I am not able to install the needed dependencies following the guidelines here,
Thanks for your kind assistance.