I run roary ( roary -e --mafft -p 32 *.gff) to produce core genome alignment on hundreds of Salmonella sequences and have results. I have the following files in the results:
I would like to visualise the panSNP tree with the roary matrix of these sequences using the command: roary_plots.py name_of_your_newick_tree_file.tre gene_presence_absence.csv. But I realise I have no .tre file in my roary outcome. How do I generate this .tre file from my sequences or from the roary outcome I have?