An empirical comparison of priority-queue and event-set implementations
Communications of the ACM
Algorithms from P to NP (vol. 1): design and efficiency
Algorithms from P to NP (vol. 1): design and efficiency
Pairing heaps: experiments and analysis
Communications of the ACM
Shortest paths algorithms: theory and experimental evaluation
Mathematical Programming: Series A and B
The influence of caches on the performance of heaps
Journal of Experimental Algorithmics (JEA)
Augment or push: a computational study of bipartite matching and unit-capacity flow algorithms
Journal of Experimental Algorithmics (JEA)
The influence of caches on the performance of sorting
SODA '97 Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms
Cache performance analysis of traversals and random accesses
Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms
LEDA: a platform for combinatorial and geometric computing
LEDA: a platform for combinatorial and geometric computing
Matrix multiplication: a case study of enhanced data cache utilization
Journal of Experimental Algorithmics (JEA)
Cut tree algorithms: an experimental study
Journal of Algorithms
Improving memory performance of sorting algorithms
Journal of Experimental Algorithmics (JEA)
Fast priority queues for cached memory
Journal of Experimental Algorithmics (JEA)
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
Analysing Cache Effects in Distribution Sorting
WAE '99 Proceedings of the 3rd International Workshop on Algorithm Engineering
Efficient Sorting Using Registers and Caches
WAE '00 Proceedings of the 4th International Workshop on Algorithm Engineering
FOCS '99 Proceedings of the 40th Annual Symposium on Foundations of Computer Science
FOCS '00 Proceedings of the 41st Annual Symposium on Foundations of Computer Science
High-Performance Algorithm Engineering for Computational Phylogenetics
The Journal of Supercomputing - Special issue on computational issues in fluid dynamics optimization and simulation
Steps toward accurate reconstructions of phylogenies from gene-order data
Journal of Computer and System Sciences - Computational biology 2002
Reconstructing optimal phylogenetic trees: a challenge in experimental algorithmics
Experimental algorithmics
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Phylogeny reconstruction from molecular data poses complex optimization problems: almost all optimization models are NP-hard and thus computationally intractable. Yet approximations must be of very high quality in order to avoid outright biological nonsense. Thus many biologists have been willing to run farms of processors for many months in order to analyze just one dataset. High-performance algorithm engineering offers a battery of tools that can reduce, sometimes spectacularly, the running time of existing phylogenetic algorithms. We present an overview of algorithm engineering techniques, illustrating them with an application to the "breakpoint analysis" method of Sankoff et al., which resulted in the GRAPPA software suite. GRAPPA demonstrated a million-fold speedup in running time (on a variety of real and simulated datasets) over the original implementation. We show how algorithmic engineering techniques are directly applicable to a large variety of challenging combinatorial problems in computational biology.