TuneTable does the same job like UPDATE STATISTICS in MS SQL Server. During its evaluation of a query, the query optimizer uses these statistics to estimate the cost of using an index to satisfy the query. Having good statistics for table cardinality and column cardinalities is very importent.

Some situations under which you should update statistics (execute TuneTable):
1) If there is significant change of data
2) If a large amount of data in an indexed column has been added, changed, or removed (that is, if the distribution of key values has changed).