Shannon and Chaol can be done with R packages (diversitySampler for Shannon which can be obtained from CRAN; mothuR for Chaol, see link).

Removing singletons: do you mean you wish to mask them or convert them to reference?

http://www.mothur.org/wiki/Main_Page

If I understand your question, you want to remove singleton from your amplicon dataset. It is typical of NGS amplicon dataset where PCR artifacts might show up during amplification or library generation. As reasoning says, why would a single unique sequence show up in million reads, if it is biological it would be amplified by the polymerase atleast say ( atleast 2 nos), it cant be that rare, that it did not amplify in a second cycle of PCR. So getting rid of singleton is suggested. 

To answer how to do it, use UPARSE pipline, to remove singleton if you like picking denovo OTU, if you use QIIME then open reference OTU picking using pick_open_reference_otus.py command actually gives you an OTU table after removing all singletons.

If QIIME is your choice you can use the QIIME scripts to do all alpha diversity calculations, if you are using UPARSE and later want to analyse the biome file in QIIME then you have to do a bit of workaround because you are using two different pipelines.

Cheers 

Thanks Rajal,

I did it.