As above, for calculation, analysis and graph.
The data is purely number.
How do I create the database table and the calculation/analysis/graph table separately? For example, I might want to create a separate table of "countif" from the database and etc.
Please suggest the name of the programme and their pro and cons as well.
Your question is very vague, In general in a RDBMS you use SQL (Structured Query Language), see here for more info http://en.wikipedia.org/wiki/SQL
A good start is a database system. Mysql and Postres are free, although there are plenty of non-free alternatives, such as Oracle and SQL Server.
The analysis and calculation is taken care of by queries, usually stored as views in with the database if they are reused often.
Beyond that, the question is too general to give any more directed advice.