Dear Peter,

here are some suggestions how to resolve binary data using NTSYSpc and how to make 3D PCoA plot using the same software.

https://www.researchgate.net/post/Any_advice_on_how_to_use_NTSYS_pc_202_software_for_genetic_diversity_analysis

Hi Peter,

You can use a genetic distance matrix of your data that you can then use to perform the PCoA in R (e.g. command 'cmdscale'. vegan package). You can use, for example, the software BioEdit to export the required distance matrix. So it's not really necessary to use binary data. Hope that helps.

GenAlex for sure! worth the try!

Regards

http://biology-assets.anu.edu.au/GenAlEx/Welcome.html

x

Hi!

Which pipeline did you use to generate the raw data?

For Qiime there are plenty of ready to use packages

For DADA2 you can follow the tutorial here:

http://evomics.org/wp-content/uploads/2016/01/phyloseq-Lab-01-Answers.html#load-packages-import-data

In my case I used an aligned nucleotide dataset (MEGA) and generated a distance matrix using MOTHUR software. MOTHUR can be used for pretty other stuff not only for 16S analysis. Then I used the distance matrix as input for PCoA analysis in R VEGAN package. It worked very well. Hope it helps,