MySQLTuner, joomla 2.5, Joins performed without indexes

# free -m

             total       used       free     shared    buffers     cached

Mem:          2006       1623        383        204        222        878

-/+ buffers/cache:        522       1483

Swap:            0          0          0

[OK] Currently running supported MySQL version 5.5.43-log
[OK] Operating on 64-bit architecture

-------- Storage Engine Statistics -------------------------------------------
[--] Status: +ARCHIVE +BLACKHOLE +CSV -FEDERATED +InnoDB +MRG_MYISAM
[--] Data in MyISAM tables: 47K (Tables: 26)
[--] Data in InnoDB tables: 25M (Tables: 386)
[--] Data in PERFORMANCE_SCHEMA tables: 0B (Tables: 17)
[--] Data in MEMORY tables: 0B (Tables: 6)
[!!] Total fragmented tables: 8

-------- Security Recommendations -------------------------------------------
[OK] All database users have passwords assigned

-------- Performance Metrics -------------------------------------------------
[--] Up for: 20h 34m 7s (101K q [1.369 qps], 3K conn, TX: 357M, RX: 35M)
[--] Reads / Writes: 72% / 28%
[--] Total buffers: 416.0M global + 960.0K per thread (100 max threads)
[OK] Maximum possible memory usage: 509.8M (25% of installed RAM)
[OK] Slow queries: 0% (0/101K)
[OK] Highest usage of available connections: 5% (5/100)
[OK] Key buffer size / total MyISAM indexes: 8.0M/2.5M
[OK] Key buffer hit rate: 99.9% (18K cached / 10 reads)
[OK] Query cache efficiency: 57.3% (36K cached / 63K selects)
[OK] Query cache prunes per day: 0
[OK] Sorts requiring temporary tables: 0% (0 temp sorts / 10K sorts)
[!!] Joins performed without indexes: 4855
[!!] Temporary tables created on disk: 46% (9K on disk / 19K total)
[OK] Thread cache hit rate: 99% (5 created / 3K connections)
[OK] Table cache hit rate: 48% (518 open / 1K opened)
[OK] Open file limit used: 2% (101/4K)
[OK] Table locks acquired immediately: 100% (67K immediate / 67K locks)
[OK] InnoDB buffer pool / data size: 256.0M/25.5M
[OK] InnoDB log waits: 0
-------- Recommendations -----------------------------------------------------
General recommendations:
Run OPTIMIZE TABLE to defragment tables for better performance
MySQL started within last 24 hours - recommendations may be inaccurate
Adjust your join queries to always utilize indexes
When making adjustments, make tmp_table_size/max_heap_table_size equal
Reduce your SELECT DISTINCT queries without LIMIT clauses
Variables to adjust:
join_buffer_size (> 256.0K, or always use indexes with joins)
tmp_table_size (> 64M)
max_heap_table_size (> 64M)

Open the phpMyAdmin configuration file config.inc.php and the uncomment the following 2 lines.
$cfg['Servers'][$i]['controluser'] = 'root';
$cfg['Servers'][$i]['controlpass'] = 'password';