What is the best software for operations optimization?

Yazan, There are a lot of tools and software ( Standard & Custom ) for operations optimization.
Based on the complexity of the operations designated, if it simple you can start off Excel, Pivot tables, Etc.
To be more accurate, What do you want to optimize? Inventory Holding time? Production time? Space? Route? It depends on the application so you can use the appropriate tool/ software.
I hope that helps :)

For optimizing operations optimizing now  a days mostly SAP is being used .

Well, personally I use the MINITAB software and Excel, both are great in Operations and Quality.
There is a powerful software such as SAS-OR if you able to use it, it would be great.