Hi, Pat
Could you explain if there is any way to generate the Principal Coodinate Analysis plot using results from UniFrac command of mothur?
I would appreciate your help.
Kim
No. Never. Never ever. Please see my 2008 ISMEJ paper, which will show you that the UniFrac test statistic is not suitable as a distance metric. There is a comment on this at http://www.mothur.org/wiki/Unifrac.unweighted and http://www.mothur.org/wiki/Unifrac.weighted.
Pat
Instead of using UniFrac distance, is there currently a way to get an OTU-based distance between different groups for Principle coordinates analysis and mantel tests?
thanks,
Jason
dist.shared will generate a phylip-formatted matrix for any of the beta-diversity measures. At some point we may add PCA and the Mantel test. I do have C++ code to generate PCA plots from phylip-formatted matrices, but the output isn’t exactly easy on the eyes. Let me know if you’re interested in testing it out.
Pat
Please let me try your C++ code to generate PCA plots from phylip-formatted matrices.
Kim
By the way, in case you didn’t notice it, I caved like a house of cards in the last release. You can now use unifrac to generate a phylip-formatted distance matrix. There’s also a PCoA command that you can use with any phylip-formatted distance matrix. I have difficulties balancing principle and market share 