This book constitutes the proceedings of the Second International Conference on Algorithms for Computational Biology, AICoB 2015, held in Mexico City, Mexico, in August 2015.The 11 papers presented in this volume were carefully reviewed and selected from 23 submissions. They were organized in topical sections named: genetic processing;

Genetic Processing.- Generalized Hultman Numbers and the Distribution of Multi-break Distances.- Implicit Transpositions in Shortest DCJ Scenarios.- Constraint-Based Genetic.- Compilation.- Molecular Recognition/Prediction P2RANK: Knowledge-Based Ligand Binding Site Prediction Using Aggregated Local Features.- StreaM - A Stream-Based Algorithm for Counting Motifs in Dynamic Graphs.- Convolutional LSTM Networks for Subcellular Localization of Proteins.- Phylogenetics.- Hybrid Genetic Algorithm and Lasso Test Approach for Inferring Well Supported Phylogenetic Trees Based on Subsets of Chloroplastic Core Genes.- Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis.- A More Practical Algorithm for the Rooted Triplet Distance.- Likelihood-Based Inference of Phylogenetic Networks from Sequence Data by PhyloDAG.- Constructing Parsimonious Hybridization Networks from Multiple Phylogenetic Trees Using a SAT-Solver.                           

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