Over at Edinburgh University, there is an awesome Molecular evolution, phylogeneticis and epidemiology's website.
On it's "epidemic" blog, run by Prof. Andrew Rambaut, there is a fantastic new primer on how to read a phylogenetic tree.
I highly recommend this for all levels of skill. It provides a great and colourful background to what a phylogenetic tree does, and does not, convey.
Of particular interest, an example includes bat and camel virus sequences. Also relevant to interpreting future MERS-CoV trees as part of the infection source/animal host debate.
These trees were drawn in FigTree (Mac and Windows versions avail,able) and polished using Adobe Illustrator.