phylogenetic tree software

Now that you know of the awesome power of the multiple sequence alignment, how can you develop models for homolog relatedness? Here are some useful tools.
Tree-puzzle: free download of maximum likelihood analysis program
Modeltest: free download of program that computes most likely maximum likelihood assumptions (of 56 possible models)
Phylogeny programs: The mother of all phylogeny software pages. A pretty comprehensive list of free, fee-based, and web-interface software for phylogenetic analysis, both distance-based and character-based. Wow.