mothur

Could I create PCoA Plot in Mothur program?


#1

Hi!

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?


#2

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.


#3

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?

Hee-Sung


#4

That approach should work.