Multiple Sequence Alignment

Editorial:These programs take multiple related sequences and align them all together, to maximise similarities, show conserved regions and provide input for phylogenetic tree drawing programs or HMM creation.
The de facto standard for protein sequence alignment, though better programs are now emerging. The above link is to Chenna Ramu's page devoted to running ClustalX on MacOS X. ClustalX gives a simple graphical interface, while ClustalW is purely command-line driven. This version has reported problems with the Tiger update to Mac OS; a Tiger compliant version is avaialble from

Derived in part from Clustal, T-Coffee offers a higher level of accuracy than Clustal, and is becoming quite popular. It is still a command-line program, and the installation instructions aren't the clearest.

Manual sequence alignment tool. Not tested, but runs on classic and OS X.