how to calculate the taxonomic Bray–Curtis dissimilarities?

[Ming Liao]

I am learning how to analyze the beta-diversity. What I knew about it was:

UniFrace distance was based on the OTU counts, while Bray-Curitis was based on the taxonomy abundance. Is that right?

I tried to use Bray-Curitis, but how to make it QIIME? 

The following writing is from one paper I read, but I am still confused how to use"beta diversity through plots.py" to get  Bray–Curtis dissimilarities, even in here http://qiime.org/scripts/beta_diversity_through_plots.html.

...both the phylogenetic weighted UniFrac distances (Lozupone et al., 2011) and the taxonomic Bray–Curtis dissimilarities (Bray & Curtis, 1957) were calculated using the beta diversity through plots.py script. This script also produced a principal coordinates analysis (PCoA) plot in which the Bray–Curtis dissimilarities between samples were used to visualize differences among groups of samples...

Any answers or comments are welcome. Thanks in advance.

Sincerely,

Ming

[Yoshiki Vázquez Baeza]

Hello Ming,

To use Bray-Curtis in beta_diversity_through_plots.py you will need to pass a parameters file (see the -p flag) with the following contents:

beta_diversity:metrics bray_curtis

Alternatively if you are using the parallel option you will need this line instead

parallel_beta_diversity:metrics bray_curtis

If you want to use bray_curtis in addition to unweighted and weighted UniFrac, the line would look like this:

parallel_beta_diversity:metrics unweighted_unifrac,bray_curtis,weighted_unifrac

To see other metrics available in QIIME try running beta_diversity.py -s

You can read more about parameters files here:

http://qiime.org/documentation/qiime_parameters_files.html

Briefly, parameters files modify the behavior of the scripts that workflow scripts execute.

Thanks!

Yoshiki.

[Ming Liao]

Thanks, Yoshiki. It was done.