I rarely have a need for global alignment (unless the proteins have been pre-trimmed to have matching domains, global alignment is usually over alignment), and I rarely have a need for all-vs-all alignment of single sequences (I get much better alignments by doing iterative search). If you are sure that you are working on the right problem, there are plenty of global aligners available. Almost all the standard tool suites include one. http://www.hku.hk/bruhk/sgaln.html contains a list of a few of the more common ones (found by googling global alignment , a task that I thought anyone who could send e-mail to these mailing lists was capable of). ------------------------------------------------------------ Kevin Karplus karplus at soe.ucsc.edu http://www.soe.ucsc.edu/~karplus Professor of Biomolecular Engineering, University of California, Santa Cruz Undergraduate and Graduate Director, Bioinformatics (Senior member, IEEE) (Board of Directors, ISCB) life member (LAB, Adventure Cycling, American Youth Hostels) Effective Cycling Instructor #218-ck (lapsed) Affiliations for identification only.