What is the best way to make a phylogeny from a list of genera?
16S phylogeny would only work for bacteria and archaea unless you are talking about mitochondrial or chloroplast 16S rRNA. Your phylogenetic marker choice should depend on which phyla you are looking at. I suggest you try using Ef-tu if your genera are highly diverse
http://www.scs.illinois.edu/schulten/tutorials/ef-tu/eftu_tutorial.pdf

Once you have a tree in Newick format, iTOL has some nice web tools for overlaying data on trees
http://itol.embl.de/itol.cgi