ClustalW ClustalW: EBI server for multiple sequence alignment on the web (Phylogenetic Analysis) http://www.ebi.ac.uk/clustalw/
Phylogeny at Pasteur Phylogeny at Pasteur: A collection of phylogenetics programs available at Pasteur Institute. Includes a number of Phylip programs. (Phylogenetic Analysis) http://bioweb.pasteur.fr/seqanal/phylogeny/intro-uk.html
SplitsTree 2 SplitsTree 2: Tool that uses split decomposition method to analyze and visualize distance data from biological sequences. (Phylogenetic Analysis) http://bibiserv.techfak.uni-bielefeld.de/splits/
Vista tools Vista tools: Multiple sequence alignment server and whole genome alignment database. (Phylogenetic Analysis) http://gsd.lbl.gov/vista/index.shtml
TreeTop TreeTop: Multiple sequence alignment based phylogenetic tree prediction program. (Phylogenetic Analysis) http://www.genebee.msu.su/services/phtree_reduced.html
GRIMM/MGR GRIMM/MGR: A tool for constructing phylogenies based on gene order for unichromosomal and multichromosomal genomes (Phylogenetic Analysis) http://nbcr.sdsc.edu/GRIMM/mgr.cgi
TreeGen TreeGen: Tree generation from distance data. [Results by email] (Phylogenetic Analysis) http://cbrg.inf.ethz.ch/Server/subsection3_1_6.html
MultAlign MultAlign: A multiple-sequence alignment program that also includes distance matrix methods for inferring trees. (Phylogenetic Analysis) http://cbrg.inf.ethz.ch/Server/MultAlign.html