Synteny Alignment To Phylogenetic Tree Using Mauve

Question

[agatorano]

Hi, I want to obtain a tree from synteny alignment of various genomes. I have been using mauve (which I believe is based on local co-linear blocks or something rather, which sounds like synteny) and can output alignment files (such as xmfa) or potentially output a "guide tree" file in newick format. I want to know, could I potentially just straight visualize the newick tree output from mauve, or should I pipeline the xmfa alignment into nexus->some bayesian inference application->visualization? Which would give a more probabilistic tree? While visualizing the newick tree from mauve seems like the rather simple approach, the user guide doesn't really give much info in terms of how it determines the tree.

[skymningen]

Mauve produces the guide tree to, well, guide the later steps of finding and extending locally collinear blocks. Therefor it does not represent the final Mauve alignment, but as fas as I know only sequence identity. So probably the idea of using the alignment files is the better choice.