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.