softwares

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http://evolution.genetics.washington.edu/phylip/software.html

Phylogeny Programs

Here are 392 phylogeny packages and 54 free web servers , (almost) all that I know about.
http://pbil.univ-lyon1.fr/software/phylowin.html Phylo_win has now been replaced by SeaView version 4 that performs both multiple sequence alignment (with muscle or clustalw2) and phylogenetic tree building (by parsimony, distances or maximum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.

Phylo_win

http://pbil.univ-lyon1.fr/software/njplot.html

NJplot

NEW: NJplot plots trees in PDF and PostScript formats (not for MacOS).