Dynamic multigrain parallelization on the cell broadband engine
Proceedings of the 12th ACM SIGPLAN symposium on Principles and practice of parallel programming
Exploring New Search Algorithms and Hardware for Phylogenetics: RAxML Meets the IBM Cell
Journal of VLSI Signal Processing Systems
Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L
Proceedings of the 2007 ACM/IEEE conference on Supercomputing
Large-scale phylogenetic analysis on current HPC architectures
Scientific Programming - Large-Scale Programming Tools and Environments
BNCOD '08 Proceedings of the 25th British national conference on Databases: Sharing Data, Information and Knowledge
PRIB '08 Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics
Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
An open source phylogenetic search and alignment package
International Journal of Bioinformatics Research and Applications
How Many Bootstrap Replicates Are Necessary?
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
Multi-granularity Parallel Computing in a Genome-Scale Molecular Evolution Application
PaCT '09 Proceedings of the 10th International Conference on Parallel Computing Technologies
Visualizing phylogenetic treespace using cartographic projections
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
A simulation study comparing supertree and combined analysis methods using SMIDGen
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
On the Use of Machine Learning to Predict the Time and Resources Consumed by Applications
CCGRID '10 Proceedings of the 2010 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing
Inferring species trees from gene duplication episodes
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
An experimental study of quartets MaxCut and other supertree methods
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
Polynomial supertree methods revisited
PRIB'10 Proceedings of the 5th IAPR international conference on Pattern recognition in bioinformatics
PPAM'09 Proceedings of the 8th international conference on Parallel processing and applied mathematics: Part II
FPGA optimizations for a pipelined floating-point exponential unit
ARC'11 Proceedings of the 7th international conference on Reconfigurable computing: architectures, tools and applications
Uncovering Hidden Phylogenetic Consensus in Large Data Sets
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The kernel of maximum agreement subtrees
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
Algorithms for rapid error correction for the gene duplication problem
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
Validation of computational prediction of horizontal gene transfer events--XenoCluster
The Journal of Supercomputing
Parallel multi-objective approaches for inferring phylogenies
EvoBIO'10 Proceedings of the 8th European conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Uncovering hidden phylogenetic consensus
ISBRA'10 Proceedings of the 6th international conference on Bioinformatics Research and Applications
Efficient relaxed search in hierarchically clustered sequence datasets
Journal of Experimental Algorithmics (JEA)
Fast Local Search for Unrooted Robinson-Foulds Supertrees
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The Kernel of Maximum Agreement Subtrees
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Proceedings of the 27th Annual ACM Symposium on Applied Computing
GTP supertrees from unrooted gene trees: linear time algorithms for NNI based local searches
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
Algorithms for knowledge-enhanced supertrees
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
A Provenance-based Adaptive Scheduling Heuristic for Parallel Scientific Workflows in Clouds
Journal of Grid Computing
TPNC'12 Proceedings of the First international conference on Theory and Practice of Natural Computing
Accounting for gene tree uncertainties improves gene trees and reconciliation inference
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
A multiobjective proposal based on the firefly algorithm for inferring phylogenies
EvoBIO'13 Proceedings of the 11th European conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
Proceedings of the 15th annual conference companion on Genetic and evolutionary computation
Embedding CIPRES science gateway capabilities in phylogenetics software environments
Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery
Proceedings of the 20th European MPI Users' Group Meeting
Performance evaluation of parallel strategies in public clouds: A study with phylogenomic workflows
Future Generation Computer Systems
Designing a parallel cloud based comparative genomics workflow to improve phylogenetic analyses
Future Generation Computer Systems
Efficient Algorithms for Knowledge-Enhanced Supertree and Supermatrix Phylogenetic Problems
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Summary: RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Γ yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets ≥4000 taxa it also runs 2--3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25 057 (1463 bp) and 2182 (51 089 bp) taxa, respectively. Availability: icwww.epfl.ch/~stamatak Contact: Alexandros.Stamatakis@epfl.ch Supplementary information: Supplementary data are available at Bioinformatics online.