on calculation of dN/dS ratio

1. HyPhy
http://www.hyphy.org/w/index.php/Main_Page

HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface) and it can be compiled as a shared library and called from other programming environments such as Python or R. HyPhy has over 7000 registered users and has been cited in over 600 peer-reviewed publications (Google Scholar). Continued development of HyPhy is currently supported in part by an NIGMS R01 award 1R01GM093939.

2. web-based tools

http://www.datamonkey.org/

3. JCoDA: a tool for detecting evolutionary selection

http://www.biomedcentral.com/1471-2105/11/284/

4. IDEA: Interactive Display for Evolutionary Analyses
http://www.biomedcentral.com/1471-2105/9/524

5. SNAP - web-based tools
http://hcv.lanl.gov/content/sequence/SNAP/SNAP.html