Per this post, in order to optimize the storage of a MyISAM table, you need to:

OPTIMIZE TABLE ;
ALTER TABLE ENGINE=MyISAM ; 
ANALYZE TABLE ;

It’s obvious what OPTIMIZE does for disk space but what does ALTER and ANALYZE do when used after OPTIMIZE? I am asking specifically about disk storage, so for example, I don’t care that ANALYZE improves join performance, etc.

That was my old ServerFault post from two years ago. Forgive me, it is slightly misworded. It should read:

As for MyISAM, you need to periodically run one of the following:

• OPTIMIZE TABLE myisam-tablename;
• ALTER TABLE myisam-tablename ENGINE=MyISAM; ANALYZE TABLE myisam-tablename;

OK, I just fixed it in ServerFault.

CLARIFICATION

OPTIMIZE TABLE tblname; performs the following:

ALTER TABLE ENGINE=MyISAM tblname; 
ANALYZE TABLE tblname;

According to the MySQL Documentation on OPTIMIZE TABLE

For MyISAM tables, OPTIMIZE TABLE works as follows:

 If the table has deleted or split rows, repair the table.

 If the index pages are not sorted, sort them.

 If the table's statistics are not up to date
(and the repair could not be accomplished by sorting the index), update them.

The last part on the table’s statistics is what ANALYZE TABLE does.

If you do not want OPTIMIZE TABLE tblname; to perform ANALYZE TABLE tblname;, then you must execute ALTER TABLE tblname ENGINE=MyISAM; instead.

WARNING : This may not be a good idea for a MyISAM that has heavy INSERTs, UPDATEs, and DELETEs because

• This will make table and index statistics stale very quickly
• Stale statistics will cause the Query Optimizer to make bad choices for query EXPLAIN plans

Please just stick with OPTIMIZE TABLE.