Phylogenetic Search Algorithms for Maximum Likelihood

[1]  J. Kim,et al.  Scaling of Accuracy in Extremely Large Phylogenetic Trees , 2000, Pacific Symposium on Biocomputing.

[2]  Seung-Jin Sul,et al.  A Randomized Algorithm for Comparing Sets of Phylogenetic Trees , 2007, APBC.

[3]  D. Wagner,et al.  Methanogenic communities in permafrost-affected soils of the Laptev Sea coast, Siberian Arctic, characterized by 16S rRNA gene fingerprints. , 2007, FEMS microbiology ecology.

[4]  O. Gascuel,et al.  Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. , 2006, Systematic biology.

[5]  Arndt von Haeseler,et al.  Simultaneous statistical multiple alignment and phylogeny reconstruction. , 2005, Systematic biology.

[6]  M. Suchard,et al.  Joint Bayesian estimation of alignment and phylogeny. , 2005, Systematic biology.

[7]  W. Fitch,et al.  Construction of phylogenetic trees. , 1967, Science.

[8]  J. Felsenstein Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.

[9]  Arndt von Haeseler,et al.  PhyNav: A Novel Approach to Reconstruct Large Phylogenies , 2004, GfKl.

[10]  D. Morrison,et al.  Increasing the efficiency of searches for the maximum likelihood tree in a phylogenetic analysis of up to 150 nucleotide sequences. , 2007, Systematic biology.

[11]  Alexandros Stamatakis,et al.  How Many Bootstrap Replicates Are Necessary? , 2009, RECOMB.

[12]  Alexandros Stamatakis,et al.  An efficient program for phylogenetic inference using simulated annealing , 2005, 19th IEEE International Parallel and Distributed Processing Symposium.

[13]  Alexandros Stamatakis,et al.  Phylogenetic models of rate heterogeneity: a high performance computing perspective , 2006, Proceedings 20th IEEE International Parallel & Distributed Processing Symposium.

[14]  A. Löytynoja,et al.  Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis , 2008, Science.

[15]  W. H. Day Optimal algorithms for comparing trees with labeled leaves , 1985 .

[16]  B. Efron Bootstrap Methods: Another Look at the Jackknife , 1979 .

[17]  David Q. Matus,et al.  Broad phylogenomic sampling improves resolution of the animal tree of life , 2008, Nature.

[18]  R. Vos,et al.  Accelerated likelihood surface exploration: the likelihood ratchet. , 2003, Systematic biology.

[19]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[20]  Olivier Gascuel,et al.  Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood , 2005, Bioinform..

[21]  Alexandros Stamatakis,et al.  Load Balance in the Phylogenetic Likelihood Kernel , 2009, 2009 International Conference on Parallel Processing.

[22]  Hanlee P. Ji,et al.  Next-generation DNA sequencing , 2008, Nature Biotechnology.

[23]  G. Olsen,et al.  Majority-Rule Consensus of Phylogenetic Trees Obtained by Maximum-Likelihood Analysis , 1997 .

[24]  Sébastien Roch,et al.  A short proof that phylogenetic tree reconstruction by maximum likelihood is hard , 2005, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[25]  D. Robinson,et al.  Comparison of phylogenetic trees , 1981 .

[26]  Thomas Ludwig,et al.  Accelerating Parallel Maximum Likelihood-Based Phylogenetic Tree Calculations Using Subtree Equality Vectors , 2002, ACM/IEEE SC 2002 Conference (SC'02).

[27]  Alexandros Stamatakis,et al.  Exploring New Search Algorithms and Hardware for Phylogenetics: RAxML Meets the IBM Cell , 2007, J. VLSI Signal Process..

[28]  Alexandros Stamatakis,et al.  Multiple evolutionary mechanisms drive papillomavirus diversification. , 2007, Molecular biology and evolution.

[29]  John P. Huelsenbeck,et al.  MrBayes 3: Bayesian phylogenetic inference under mixed models , 2003, Bioinform..

[30]  M. Donoghue,et al.  Rates of Molecular Evolution Are Linked to Life History in Flowering Plants , 2008, Science.

[31]  H. Philippe,et al.  A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. , 2004, Molecular biology and evolution.

[32]  J. Rougemont,et al.  A rapid bootstrap algorithm for the RAxML Web servers. , 2008, Systematic biology.

[33]  Ziheng Yang PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[34]  Nina Amenta,et al.  A Linear-Time Majority Tree Algorithm , 2003, WABI.

[35]  M. Ragan,et al.  Is Multiple-Sequence Alignment Required for Accurate Inference of Phylogeny? , 2007, Systematic biology.

[36]  Tandy J. Warnow,et al.  Sequence-Length Requirements for Phylogenetic Methods , 2002, WABI.

[37]  A. Rodrigo,et al.  Likelihood-based tests of topologies in phylogenetics. , 2000, Systematic biology.

[38]  Thomas Ludwig,et al.  A fast program for maximum likelihood-based inference of large phylogenetic trees , 2004, SAC '04.

[39]  Thomas Ludwig,et al.  RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees , 2005, Bioinform..

[40]  Bastien Boussau,et al.  Efficient likelihood computations with nonreversible models of evolution. , 2006, Systematic biology.

[41]  Michael H. Goldwasser,et al.  Data structures, near neibor searches, and methodology : fifth and sixth DIMACS implementation challenges : papers related to the DIMACS challenge on dictionaries and priority queues (1995-1996) and the DIMACS challenge on near neighbor searches (1998-1999) , 2002 .

[42]  K. Strimmer,et al.  TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics , 2004, BMC Evolutionary Biology.

[43]  Alexandros Stamatakis,et al.  Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures , 2008, Philosophical Transactions of the Royal Society B: Biological Sciences.

[44]  Sergei L. Kosakovsky Pond,et al.  Column sorting: rapid calculation of the phylogenetic likelihood function. , 2004, Systematic biology.

[45]  Alexandros Stamatakis,et al.  Exploiting Fine-Grained Parallelism in the Phylogenetic Likelihood Function with MPI, Pthreads, and OpenMP: A Performance Study , 2008, PRIB.

[46]  Alexandros Stamatakis,et al.  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..

[47]  D. Pearl,et al.  Stochastic search strategy for estimation of maximum likelihood phylogenetic trees. , 2001, Systematic biology.

[48]  Arndt von Haeseler,et al.  pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies , 2005, Bioinform..

[49]  J. Felsenstein CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

[50]  Bernard M. E. Moret,et al.  Efficiently Computing the Robinson-Foulds Metric , 2007, J. Comput. Biol..

[51]  Thomas Ludwig,et al.  AxML: a fast program for sequential and parallel phylogenetic tree calculations based on the maximum likelihood method , 2002, Proceedings. IEEE Computer Society Bioinformatics Conference.

[52]  Srinivas Aluru,et al.  Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L , 2007, Proceedings of the 2007 ACM/IEEE Conference on Supercomputing (SC '07).

[53]  M. Rosenberg,et al.  Multiple sequence alignment accuracy and phylogenetic inference. , 2006, Systematic biology.

[54]  Derrick J. Zwickl Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion , 2006 .

[55]  Alexandros Stamatakis,et al.  Distributed and parallel algorithms and systems for inference of huge phylogenetic trees based on the maximum likelihood method , 2004 .

[56]  James C. Wilgenbusch,et al.  AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics , 2008, Bioinform..

[57]  Ziheng Yang Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods , 1994, Journal of Molecular Evolution.

[58]  D. Hoyle,et al.  RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods. , 2001, Genetics.

[59]  Hideo Matsuda,et al.  fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood , 1994, Comput. Appl. Biosci..