http://evolution.genetics.washington.edu/phylip/programs.html
... by type of data
•DNA sequences 
•Protein sequences 
•Restriction sites 
•Distance matrices 
•Gene frequencies 
•Quantitative characters 
•Discrete characters 
•tree plotting, consensus trees, tree distances and tree manipulation
... by type of algorithm
•Heuristic tree search 
•Branch-and-bound tree search 
•Interactive tree manipulation 
•Plotting trees, consenus trees, tree distances 
•Converting data, making distances or bootstrap replicates
Get Programs
Clustalw
Sequence alignment and trimming