8.9 years ago by
Using online systems isn't always the fastest way to achieve results, although it is generally much easier, as you are using a web interface to control the program inputs. If you are able to use your command terminal, then you can download binaries that will give you your results much faster (depending on the machine specs of course).
I'd use MAFFT as my first choice, or MUSCLE comes a close second (although FastTree recommends it), for building the alignments. However, I'd recommend FastTree over PhyML for building the trees.
FastTree approximates to maximum-likelihood, performing heuristic neighbour-joining using a minimal model of evolution, before maximizing the trees likelihood as detailed here. It also takes input in FASTA format, which means you don't need to convert to PHYLIP format, as with PhyML or PHYLIP.