Phylogeny and comparative genomics - Phylo_win
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.
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.