Phylogentic tree construction using only the synonymous sites

Question

[vicky]

Hi

Do any one knows any program other than Mega (Phylogenetic package) which can make phylogenetic tree only considering synonymous sites?

Thanks

Answer 1

[Josh Herr]

For the most part, any phylogenetic program or package will let you make a tree out of any data that you would like. I'm not a big fan of the MEGA program, but here is a good list of tools. For example, in a nexus file you can mask any site you would like from the data analysis. You can also weight certain sites if you have reason to believe they are more informative than other sites.

As far as synonymous sites -- why would you want to use them? If you only consider sites that are the same across all the taxa in your matrix you will not have any signal to resolve a phylogenetic tree.

Am I misunderstanding your question?

[vicky]

Thanks of the reply. In the sea-view http://pbil.univ-lyon1.fr/software/seaview3.html , I found that in NJ method you can consider the Ks sites to construct the tree. Regarding why I want to use that, one of the reviewers of my paper asked for it. He believes that divergence time gets affected if I don't consider codon identity or fold-degeneration into account.

[Josh Herr]

OK, I get it... I was confused by the "only synonymous sites" in your original question. I'm still not exactly clear on what you are trying to do, but it's to take synonymous sites into consideration not to use only synonymous sites.