Phylo_win has now been replaced by SeaView version 4 that performs both multiple sequence alignment (with muscle or clustalw2) and phylogenetic tree building (by parsimony, distances or maximum likelihood) for DNA or protein sequences.
Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution 27(2):221-224.
Phylo_win is nevertheless still available here.
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