Dear Utkarsh, bootstrapping can be performed by RStudio (https://www.rstudio.com/). But i am sure it's not the only one (free available) software for bootstrapping.

I am sure you can do it in R: http://www.r-project.org/

you can use a variety of software,

STATA, R, GAMS, and even spreed sheet (Excel).

Dear sir,

You can use Stata, Eviews and Shazam to run Bootstrap.

But there's the point that with this software you can not get the corrected bias estimators for each DMUs.

So, I suggest using the Excel software. In this software, you must use the correct command to get the corrected bias estimators and then try to estimate the distances.

  In the this regard, I sent you an attachment file that can help you with this.

I hope it could help...

Alireza