We are pleased to present the proceedings of the Second Workshop on Al- rithms in Bioinformatics (WABI 2002), which took place on September 17-21, 2002 in Rome, Italy. The WABI workshop was part of a three-conference me- ing, which, in addition to WABI, included the ESA and APPROX 2002. The three conferences are jointly called ALGO 2002, and were hosted by the F- ulty of Engineering, University of Rome "La Sapienza." Seehttp: //www.dis. uniroma1.it/ algo02 for more details. The Workshop on Algorithms in Bioinformatics covers research in all areas of algorithmic work in bioinformatics and...