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: 

1. gene_presence_absence.csv
2. gene_presence_absence.Rtab
3. pan_genome_reference.fa
4.  accessory_binary_genes.fa.newick
5. accessory_graph.dot
6.  core_accessory_graph.dot
7.  core_gene_alignment.aln
8.  clustered_proteins

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?


you can use a program like FastTree where you input the core_gene.aln file and it outputs the Newick tree file 

fasttree core_gene.aln > tree.file 

http://www.microbesonline.org/fasttree/