Shannon & Chao1 Index FAQ
I would like more information about the Shannon and Chao1 index. What papers can I read?
Here are some helpful papers:
Tuomisto, H. (2010). A diversity of beta diversities: straightening up a concept gone awry. Part 1. Defining beta diversity as a function of alpha and gamma diversity". Ecography, 33, 2-22.
Chao A. Non-parametric estimation of the number of classes in a population. Scand J Stat. 1984;11:265–270.
How is H' calculated?
File:Shannon Index Equation.gif
N is the number of individuals
E is the evenness of the diversity
Can I input multiple samples?
Yes. Submit a zip file containing the individual clustering files, each of which derive from a sample.
I input a .tgz file but the tool does not work properly. What should I do?
The .tgz file downloaded as clustering results contains files of different types in addition to .clust files. You need to uncompress it with a tool such as 7-zip and upload only the .clust files for this tool.
"Does this tool process multiple .clust files?"
Yes. This tool calculates Shannon and Chao1 abundance estimates by each sample from input .clust file(s). Therefore, no duplicate sample names are allowed, i.e. all sample names have to be unique among all the uploaded .clust files or an error message will show up.