roary_plots: pangenome matrix tree does not look like input.newick tree

[mcclaudi]

Could anybody enlighten me as to how to figure out which genome is which in the pangenome matrix plot after using roary_plots?
I have built a tree from the core_gene_alignment.aln file using fasttree, which was then used as the input for roary_plots analysis. However, the phylogenetic tree in the pangenome matrix does not look anything like the tree used as the input (?)!
Many thanks,
Claudia

[mcclaudi]

update: just used a different tree viewer, and this time the trees overlap...