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Here are 392 phylogeny packages and 54 free web servers , (almost) all that I know about.
Ziheng Yang Table of contents
Phylo_win has now been replaced by SeaView version 4 that performs both multiple sequence alignment (with muscle or clustalw2) and phylogenetic tree building (by parsimony, distances or maximum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. Reference : Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building.
NEW: NJplot plots trees in PDF and PostScript formats (not for MacOS).