Table 1. An overview of tools available in the Toolkit.

Category	Tools
Search	CS-BLAST (6), HHblits (7), HHpred (5), HHsenser (45), HMMER3 (46), PatternSearch, ProtBLAST (9), ProtBLAST+ (15), PSI-BLAST (14), PSI-BLAST+ (15), SimShiftDB (47), PDBalert (37)
Alignment	AlignmentViewer, Blammer, Clustal Omega (38), GLProbs (42), HHalign, Kalign (39), MAFFT (48), MSAProbs (40), MUSCLE (49), ProbCons (50), TCoffee (41)
Sequence Analysis	Aln2Plot, COILS/PCOILS (8), FRpred (51), HHrep (25), HHrepID (13), MARCOIL (11), REPPER (52), TPRpred (53)
Secondary Structure	Ali2D, HHomp (30), Quick2D
Tertiary Structure	bFit (54), HHfrag (55), HHpred (5), Modeller (10), SamCC (31)
Classification	ANCESCON (12), BLASTClust (9), CLANS (56), ClubSub-P (57), daTAA (28), GCView (58), HHcluster (27), PHYLIP-NEIGHBOR (59)
Utilities	6FrameTranslation, Backtranslator, Extract GIs, GI2Promoter, HHfilter, Reformat, RetrieveSeq

The categories listed here correspond to the section tabs in the menu bar located at the top of the Toolkit page. Section-specific tools are listed in a submenu within each tab. All tools can also be accessed through the tool index displayed on the homepage of the Toolkit. Tools developed by us are shown in boldface and tools added since our last publication on the Toolkit in 2006 are underlined.