Some Bio Toolkits

http://emboss.sourceforge.net/apps/cvs/emboss/apps/remap.html

http://www.ngbw.org/about_dev.php

Also to look at:

http://www.icir.org/christian/libstree/

http://www.cs.ucdavis.edu/~gusfield/strmat.html

http://hkn.eecs.berkeley.edu/~dyoo/python/suffix_trees/