I want to konw how to convert a general treefile to a ultrametric treefile. I have maken a species tree using RAxML to analysis several hundreds single copy genes. And now, i need to use CAFE to analysis the protein families expansion. But CAFE need a Newick treefile as input. Could anyone give a suggestion?
If you need to convert just one tree from Nexus to Newick, the simplest thing might be just to open it up in a tree-viewing program like FigTree (http://tree.bio.ed.ac.uk/software/figtree/), and export as a Newick: File > Save Trees > Select 'Newick' from menu.
Newick treefiles are of course not necessarily ultrametric, but you can convert your tree into a cladogram (a tree with all branch lengths = 1, which is what I think you might mean) using the options within FigTree: Trees > Transform Branches > Select 'Cladogram'.