Unfortunately, I don't know any specific software to calculate sediment indexes for HM. However, you could use MS Excel. Just put your raw data and calculate the indexes according to their specific formula. Here you may create a macros to automate the process. Thus, you will have your own software for specific purposes.
As an option you could also use Surfer software or StatSoft to transform your data with diferent equations.
I would suggest you to calculate them manually, so that the trends and important characteristics are engrained in the minds of the researcher.
That said, I would suggest you to look for the publications of M.P.Jonathan and R.Nagarajan who have published extensively on these topics of your interest.
You don't need any software programs, you can calculate them by using excel or calculator, you will need references values or the Local background values of your study area, (Environmental indexes : Enrichment factor, Geo accumulation index, Contamination factor...)
Here enclosed, you can find my paper research about the asseement of contamination level by metals, by using environmental indexes
To calculate pollution indices of Heavy metals you can just go through these paper.
Ranjan, R. K., Sinha, A. K., Gupta, D., Sappal, S. M., Kumar, A., & Ramanathan, A. L. (2016). Sedimentary Geochemistry of Kabar Tal Wetland, Begusarai, Bihar, India. Journal of Applied Geochemistry, 18(4), 414.
Thank you very much Nezha mejjad for your kind reply. Could you kind enough to specify me that from where we will get the need references values or the Local background values of a particular study area ?