Percona Toolkit
pt-duplicate-key-checker
Find duplicate indexes and foreign keys on MySQL tables.
Find duplicate indexes on a database:
pt-duplicate-key-checker -d database
pt-index-usage
Read queries from a log and analyze how they use indexes.
pt-index-usage /var/log/mysql/mysql-slow.log
pt-mysql-summary
pt-variable-advisor
Check MySQL configuration for suggested changes.
pt-query-advisor
Analyze queries and advise on possible problems.