Ka/Ks Tutorial for DataMonkey

DataMonkey is a good internet tool to calculate Ka/ks by using Yang package. It incorporates many methods such as SLAC, FEL, etc, and also some popular assumption, like HKY85-F84. Also DataMonkey is a codon-based software, and you can get positive selection in codon levels. Below are the steps showing you how to get Ka/Ks in DataMonkey.

1. go to the home page of DataMonkey(http://www.datamonkey.org/) and select "ANALYZE YOUR DATA".
2. choose file in the right format and upload your data.

3. A basic analyse will show up. Then select "Proceed to the analysis menu".

4. You can see a combobox in "Method", choose "SLAC" and press "run".

5. You can see a updating page in 30 seconds. It will show you Ka/Ks.

6. Then you select "INFORMATION: OTHER ANALYSIS" to get more information. You can get "Neighbor Joining Tree" from this page. You can also re-analyze your data by another method. all the result will keep in this page.

7. For example, you want to analyze your data by "FEL".

8.  Do the same steps as "SLAC".

9.  From "INFORMATION: OTHER ANALYSIS" page, you can see both results from "SLAC" and "FEL".

10. AT last, you can integrate both results and get a final report.