Could I create PCoA Plot in Mothur program?



I had sequences of functional gene name hgcA associated with mercury methylation, which were obtained from environmental samples using clone libraries. Could I make PCoA plot in Mothur program?


Certainly - we have a command called pcoa that will do it for you. You can see how we use it in the MiSeq SOP page.


Thanks for your quick reply.

My seqs are not from 16S gene, but from a functional genes, which were obtained clone libraries from several different environmental samples. I would like to get PCoA plot to see how different the phylogenetic relationship between samples. I would like to use Unfrac weighted distance matrix for getting PCoA plot.

I just guess that I have to obtained Unifrac weighted distance matrix from phylogenetic tree that was constructed using my sequence. Then, I may use the matrix to generate PCoA plot.

Do you think this pathway is work?



That approach should work.