PCoA data visualization

Hi,

I am a beginner and using Mothur to analyze 16S pyrosequence data.

I have generated the dist, axes and loading files for PCoA analysis. Please guide me how to visualize or plot the data in 3d. I highly appreciate any help.

Thanks
Nazia

Sure - the axes file contains the data that you want to plot. You can use Excel, R, or whatever to plot the first 2 or 3 axes. The loadings file will tell you what percentage of the overall variation those axes explain.

HTH,
Pat