http://www.phylogeny.fr/
Robust Phylogenetic Analysis For The Non-Specialist
http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/
Phylogeny @EBI. Commonly used phylogenetic tree generation methods provided by the ClustalW2 program.
Much more tools available @ http://www.ebi.ac.uk/services
http://www.st-va.ncbi.nlm.nih.gov/tools/cobalt/re_cobalt.cgi?
Cobalt Constraint-based Multiple Protein Alignment Tool @NCBI.
http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/