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This book constitutes the proceedings of the Third International Conference on Algorithms for Computational Biology, AlCoB 2016, held in Trujillo, Spain, in June 2016. § The 13 full papers presented in this volume were carefully reviewed and selected from 23 submissions. They are organized in the following topical sections: biological networks and modelling; biological structure processing; phylogenetics; and sequence analysis and rearrangement. In addition one invited talk is included.