• DAMBE: Data Analysis in Molecular Biology and Evolution (for Windows)
• MEGA: Molecular Evolutionary Genetic Analysis (for Windows, DOS and Mac)
• NOVA
• PAML: Phylogenetic Analysis by Maximum Likelihood
• PHYLIP: package of programs for inferring phylogenies (University of Washington, USA)
• PAUP*:
• TNT
• TREE-PUZZLE: maximum likelihood analysis for nucleotide, amino acid, and two-state data

And more programs can be found Here.

Here list some useful tools.

• Seq-Gen