Hi!

You can use vegan package from R. There are severel diversity indeces with explanations.

http://cran.r-project.org/web/packages/vegan/vignettes/diversity-vegan.pdf

Thanks Robert

You can use ADZE, DAPC-R, DIYABC, Genetix, GenoDive, Multilocus, PopGene, etc.

thanks Hu

you can use SDR (Species diversity and Richness) software, if you want a free software i offer PAST software, if you not familiar with R language i suggest you can use BiodiversityR package in R, and if you are, use Vegan package.

for more information read the file and use the scripts.

Good Luck,

Baqer.

http://www.worldagroforestry.org/downloads/publications/PDFs/B13695.pdf

http://www.worldagroforestry.org/sites/default/files/BiodiversityR/Scripts.zip

Thanks Mohammad

I like this one.

http://www.sams.ac.uk/peter-lamont/biodiversity-pro

Indeces like Shannon-Weiner or Simpson can also be calculated in Excel. On youtube there are great tutorial videos for this.

For more complicated methods I thnk R is the best. It can be adjusted and tuned to your needs and requests of the task you are working on. Also - as it was written before - different packages are available in this environment.

Dear Peter,

What I need was Beta, gamma and alpha diversity. I want to  know the most best software, I think PAST and BiodiversityPro are more friendly.

Thanks

Mega software can calculate the diversity and its freely available.

Many thanks to all of you

You can use PAST for free

thanks Bjorn, very helpful

Dear Arshad,

Try entropart: The decomposition of similarity-based diversity and its bias

correction

vegan in R

Biodiversity Pro