Phylo_win is a graphical colour interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony and maximum likelihood methods and bootstrap with any of them. Many distances can be used including Jukes & Cantor, Kimura, Tajima & Nei, HKY, Galtier & Gouy (1995), LogDet for nucleotidic sequences, Poisson correction for protein sequences, Ka and Ks for codon sequences. Species and sites to include in the analysis are selected by mouse. Reconstructed trees can be drawn, edited, printed, stored and evaluated according to numerous criteria.

Use of Phylo_win

Taxonomic species groups and sets of conserved regions can be defined using mouse and stored into sequence files, thus avoiding multiple data files. The program is entirely mouse-driven. On-line help makes it easy to use. Most usual sequence file formats in phylogeney can be read: CLUSTAL, FASTA, PHYLIP and MASE. A screen shot of the main window is available here.

Download Phylo_win

Phylo_win can be downloaded through our FTP server. You may also use the following table to directly access the version corresponding to your architecture:

MS Windows


MacOS (8,9)




Tru64 Unix

SGI 6.2

If you download Phylo_win, please register by e-mail to Nicolas Galtier. Any comment or suggestion are welcome.


Also, if you use Phylo_win in a published work, please cite the following reference:
Galtier, N., Gouy, M. and Gautier, C. (1996) SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phylogeny. Comput. Applic. Biosci., 12, 543-548.

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