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This book constitutes the refereed proceedings of the 6th International Workshop on Algorithms in Bioinformatics, WABI 2006, held in Zurich, Switzerland in September 2006 in the course of the ALGO 2006 conference meetings. The 36 revised full papers presented were carefully reviewed and selected from 100 submissions. All current issues of algorithms in bioinformatics are addressed, ranging from mathematical tools to experimental studies of approximation algorithms and reports on significant computational analyses. Numerous biological problems are dealt with, including genetic mapping, sequence alignment and sequence analysis, phylogeny, comparative genomics, and protein structure. For the first time also machine-learning approaches along with combinatorial optimization are covered.