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ClustalW
EBI server for multiple sequence alignment on the web
GRIMM/MGR
A tool for constructing phylogenies based on gene order for unichromosomal and multichromosomal genomes
MultAlign
A multiple-sequence alignment program that also includes distance matrix methods for inferring trees.
Phylogeny at Pasteur
A collection of phylogenetics programs available at Pasteur Institute. Includes a number of Phylip programs.
SplitsTree 2
Tool that uses split decomposition method to analyze and visualize distance data from biological sequences.
TreeGen
Tree generation from distance data. [Results by email]
TreeTop
Multiple sequence alignment based phylogenetic tree prediction program.
Vista tools
Multiple sequence alignment server and whole genome alignment database.