**10**wrote:

Hi all,

I have a relatively simple question. I'm trying to perform a dn/ds analysis on a set of 11 nucleotide sequences that I have. The sequences are aligned (by ClustalW in MegAlign) and are specifically those for a particular protein of interest. I know paml is the standard for the dn/ds analysis, but I find it quite bewildering, so I'm attempting to solve my problem with Matlab, which I feel more comfortable using. However, it seems that Matlab can only perform a dn/ds calculation on two sequences at a time (see: http://www.mathworks.com/help/bioinfo/ref/dnds.html ). This is obviously not conducive to what I want to do, so I was wondering, is there a way to handle more than two sequences with this command in Matlab?

Any help would be appreciated! I'm just starting to dip my feet into bioinformatics, and I need all the help I can get.

**8.4k**• written 6.1 years ago by munna.uppal •

**10**

You might wanna try PAML anyway. Looks like the MATLAB function doesn't lend itself to flexibility, and unless you dive in, you'll never know how much fun command line tools are!

People here should be able to help you with most errors/difficulties you encounter learning any new tool.

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