-
1
-
-
0035153070
-
Pyrosequencing sheds light on dna sequencing
-
M. Ronaghi, "Pyrosequencing Sheds Light on DNA Sequencing,": Genome Research, vol. 11, no. 1, pp. 3-11, 2001.
-
(2001)
Genome Research
, vol.11
, Issue.1
, pp. 3-11
-
-
Ronaghi, M.1
-
2
-
-
0025879424
-
Complementary DNA sequencing: Expressed sequence tags and human genome project
-
M. Adams, J. Kelley, J. Gocayne, M. Dubnick, M. Polymeropoulos, H. Xiao, C. Merril, A. Wu, B. Olde, R. Moreno et al. "Complementary DNA sequencing: Expressed sequence tags and human genome project,": Science, vol. 252, no. 5013, pp. 1651-1656, 1991.
-
(1991)
Science
, vol.252
, Issue.5013
, pp. 1651-1656
-
-
Adams, M.1
Kelley, J.2
Gocayne, J.3
Dubnick, M.4
Polymeropoulos, M.5
Xiao, H.6
Merril, C.7
Wu, A.8
Olde, B.9
Moreno, R.10
-
3
-
-
57149107977
-
Introduction. Statistical and computational challenges in molecular phylogenetics and evolution
-
N. Goldman and Z. Yang, "Introduction. Statistical and computational challenges in molecular phylogenetics and evolution,": Phil. Trans. R. Soc. series B, Biol. Sci., vol. 363, no. 1512, p. 3889, 2008.
-
(2008)
Phil. Trans. R. Soc. series B, Biol. Sci.
, vol.363
, Issue.1512
, pp. 3889
-
-
Goldman, N.1
Yang, Z.2
-
4
-
-
33746047855
-
The design, implementation, and evaluation of mpiBLAST
-
A. Darling, L. Carey, and W. Feng, "The Design, Implementation, and Evaluation of mpiBLAST,": Proceedings of ClusterWorld, vol. 2003, 2003.
-
(2003)
Proceedings of ClusterWorld
, vol.2003
-
-
Darling, A.1
Carey, L.2
Feng, W.3
-
5
-
-
38049165771
-
AxPcoords & parallel axparafit: Statistical co-phylogenetic analyses on thousands of taxa
-
A. Stamatakis, A. Auch, J. Meier-Kolthoff, and M. Göker, "AxPcoords & Parallel AxParafit: Statistical Co-Phylogenetic Analyses on Thousands of Taxa,": BMC Bioinformatics, vol. 8, 2007.
-
(2007)
BMC Bioinformatics
, vol.8
-
-
Stamatakis, A.1
Auch, A.2
Meier-Kolthoff, J.3
Göker, M.4
-
6
-
-
0000461280
-
Confidence limits on phylogenies: An approach using the bootstrap
-
J. Felsenstein, "Confidence Limits on Phylogenies: An Approach Using the Bootstrap,": Evolution, vol. 39, no. 4, pp. 783-791, 1985.
-
(1985)
Evolution
, vol.39
, Issue.4
, pp. 783-791
-
-
Felsenstein, J.1
-
7
-
-
34548451343
-
Large maximum likelihood trees
-
B. Minh, L. Vinh, H. Schmidt, and A. Haeseler, "Large maximum likelihood trees,": In Proc. of the NIC Symposium 2006, 2006, pp. 357-365.
-
(2006)
Proc. of the NIC Symposium 2006
, pp. 357-365
-
-
Minh, B.1
Vinh, L.2
Schmidt, H.3
Haeseler, A.4
-
8
-
-
34748917568
-
Dynamic multigrain parallelization on the cell broadband engine
-
San Jose, CA, March
-
F. Blagojevic, D. Nikolopoulos, A. Stamatakis, and C. Antonopoulos, "Dynamic Multigrain Parallelization on the Cell Broadband Engine,": In Proc. of PPoPP 2007, San Jose, CA, March 2007.
-
(2007)
Proc. of PPoPP 2007
-
-
Blagojevic, F.1
Nikolopoulos, D.2
Stamatakis, A.3
Antonopoulos, C.4
-
9
-
-
26844521242
-
RAxML-OMP: An efficient program for phylogenetic inference on SMPs
-
A. Stamatakis, M. Ott, and T. Ludwig, "RAxML-OMP: An Efficient Program for Phylogenetic Inference on SMPs.": PaCT, pp. 288-302, 2005.
-
(2005)
PaCT
, pp. 288-302
-
-
Stamatakis, A.1
Ott, M.2
Ludwig, T.3
-
10
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
J. Felsenstein, "Evolutionary trees from DNA sequences: A maximum likelihood approach,": J. Mol. Evol., vol. 17, pp. 368-376, 1981.
-
(1981)
J. Mol. Evol.
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
11
-
-
27144503359
-
PIQPNNI: Parallel reconstruction of large maximum likelihood phylogenies
-
B. Minh, L. Vinh, A. Haeseler, and H. Schmidt, "pIQPNNI: Parallel reconstruction of large maximum likelihood phylogenies,": Bioinformatics, vol. 21, no. 19, pp. 3794-3796, 2005.
-
(2005)
Bioinformatics
, vol.21
, Issue.19
, pp. 3794-3796
-
-
Minh, B.1
Vinh, L.2
Haeseler, A.3
Schmidt, H.4
-
12
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
S. Guindon and O. Gascuel, "A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.": Syst. Biol., vol. 52, no. 5, pp. 696-704, 2003.
-
(2003)
Syst. Biol.
, vol.52
, Issue.5
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
13
-
-
28944447963
-
Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood
-
W. Hordijk and O. Gascuel, "Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood,": Bioinformatics, vol. 21, no. 24, pp. 4338-4347, 2005.
-
(2005)
Bioinformatics
, vol.21
, Issue.24
, pp. 4338-4347
-
-
Hordijk, W.1
Gascuel, O.2
-
15
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed model
-
F. Ronquist and J. Huelsenbeck, "MrBayes 3: Bayesian phylogenetic inference under mixed models,": Bioinformatics, vol. 19, no. 12, pp. 1572-1574, 2003.
-
(2003)
Bioinformatics
, vol.19
, Issue.12
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.2
-
16
-
-
13444259388
-
TREEFINDER: A powerful graphical analysis environment for molecular phylogenetics
-
G. Jobb, A. Haeseler, and K. Strimmer, "TREEFINDER: A powerful graphical analysis environment for molecular phylogenetics,": BMC Evol. Biol., vol. 4, 2004.
-
(2004)
BMC Evol. Biol.
, vol.4
-
-
Jobb, G.1
Haeseler, A.2
Strimmer, K.3
-
17
-
-
0036205377
-
TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
-
H. Schmidt, K. Strimmer, M. Vingron, and A. Haeseler, "TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing,": Bioinformatics, vol. 18, pp. 502-504, 2002.
-
(2002)
Bioinformatics
, vol.18
, pp. 502-504
-
-
Schmidt, H.1
Strimmer, K.2
Vingron, M.3
Haeseler, A.4
-
18
-
-
0029836454
-
Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies
-
K. Strimmer and A. Haeseler, "Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies,": Mol. Biol. Evol., vol. 13, pp. 964-969, 1996.
-
(1996)
Mol. Biol. Evol.
, vol.13
, pp. 964-969
-
-
Strimmer, K.1
Haeseler, A.2
-
20
-
-
16344387501
-
DPRml: Distributed phylogeny reconstruction by maximum likelihood
-
T. Keane, T. Naughton, S. Travers, J. McInerney, and G. Mc-Cormack, "DPRml: Distributed Phylogeny Reconstruction by Maximum Likelihood,": Bioinformatics, vol. 21, no. 7, pp. 969-974, 2005.
-
(2005)
Bioinformatics
, vol.21
, Issue.7
, pp. 969-974
-
-
Keane, T.1
Naughton, T.2
Travers, S.3
McInerney, J.4
Mc-Cormack, G.5
-
21
-
-
34548633617
-
New approaches to phylogenetic tree search and their application to large numbers of protein alignments
-
S. Whelan, "New Approaches to Phylogenetic Tree Search and Their Application to Large Numbers of Protein Alignments,": Syst. Biol., vol. 56, no. 5, pp. 727-740, 2007.
-
(2007)
Syst. Biol.
, vol.56
, Issue.5
, pp. 727-740
-
-
Whelan, S.1
-
22
-
-
33750403801
-
RAxML-VI-HPC: Maximum likelihoodbased phylogenetic analyses with thousands of taxa and mixed models
-
A. Stamatakis, "RAxML-VI-HPC: Maximum likelihoodbased phylogenetic analyses with thousands of taxa and mixed models,": Bioinformatics, vol. 22, no. 21, pp. 2688-2690, 2006.
-
(2006)
Bioinformatics
, vol.22
, Issue.21
, pp. 2688-2690
-
-
Stamatakis, A.1
-
23
-
-
14644397888
-
RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees
-
A. Stamatakis, T. Ludwig, and H. Meier, "RAxML-III: A Fast Program for Maximum Likelihood-based Inference of Large Phylogenetic Trees,": Bioinformatics, vol. 21(4), pp. 456-463, 2005.
-
(2005)
Bioinformatics
, vol.21
, Issue.4
, pp. 456-463
-
-
Stamatakis, A.1
Ludwig, T.2
Meier, H.3
-
24
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
Z. Yang, "PAML 4: Phylogenetic Analysis by Maximum Likelihood,": Molecular Biology and Evolution, vol. 24, no. 8, p. 1586, 2007.
-
(2007)
Molecular Biology and Evolution
, vol.28
, Issue.8
, pp. 1586
-
-
Yang, Z.1
-
27
-
-
56849127431
-
Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/l
-
M. Ott, J. Zola, S. Aluru, and A. Stamatakis, "Large-scale Maximum Likelihood-based Phylogenetic Analysis on the IBM BlueGene/L,": In Proc. of IEEE/ACM Supercomputing Conference 2007 (SC2007), 2007.
-
(2007)
Proc. of IEEE/ACM Supercomputing Conference 2007 (SC2007)
-
-
Ott, M.1
Zola, J.2
Aluru, S.3
Stamatakis, A.4
-
28
-
-
57049132751
-
Exploiting fine-grained parallelism in the phylogenetic likelihood function with MPI, pthreads, and openMP: A performance study
-
ser. Lecture Notes in Computer Science, M. Chetty, A. Ngom, and S. Ahmad, Eds., Springer
-
A. Stamatakis and M. Ott, "Exploiting Fine-Grained Parallelism in the Phylogenetic Likelihood Function with MPI, Pthreads, and OpenMP: A Performance Study.": In PRIB, ser. Lecture Notes in Computer Science, M. Chetty, A. Ngom, and S. Ahmad, Eds., vol. 5265. Springer, 2008, pp. 424-435.
-
(2008)
PRIB
, vol.5265
, pp. 424-435
-
-
Stamatakis, A.1
Ott, M.2
-
29
-
-
42149157760
-
Broad phylogenomic sampling improves resolution of the animal tree of life
-
C. Dunn, A. Hejnol, D. Matus, K. Pang, W. Browne, S. Smith, E. Seaver, G. Rouse, M. Obst, G. Edgecombe, M. Sorensen, S. Haddock, A. Schmidt-Rhaesa, A. Okusu, R. Kristensen, W. Wheeler, M. Martindale, and G. Giribet, "Broad phylogenomic sampling improves resolution of the animal tree of life,": Nature, vol. 452, no. 7188, pp. 745-749, 2008.
-
(2008)
Nature
, vol.452
, Issue.7188
, pp. 745-749
-
-
Dunn, C.1
Hejnol, A.2
Matus, D.3
Pang, K.4
Browne, W.5
Smith, S.6
Seaver, E.7
Rouse, G.8
Obst, M.9
Edgecombe, G.10
Sorensen, M.11
Haddock, S.12
Schmidt-Rhaesa, A.13
Okusu, A.14
Kristensen, R.15
Wheeler, W.16
Martindale, M.17
Giribet, G.18
-
30
-
-
34547754024
-
Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates
-
J. Hackett, H. Yoon, S. Li, A. Reyes-Prieto, S. Rummele, and D. Bhattacharya, "Phylogenomic Analysis Supports the Monophyly of Cryptophytes and Haptophytes and the Association of Rhizaria with Chromalveolates,": Molecular Biology and Evolution, vol. 24, no. 8, p. 1702, 2007.
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.8
, pp. 1702
-
-
Hackett, J.1
Yoon, H.2
Li, S.3
Reyes-Prieto, A.4
Rummele, S.5
Bhattacharya, D.6
-
31
-
-
40749116835
-
Phylogenomics reshuffles the eukaryotic supergroups
-
F. Burki, K. Shalchian-Tabrizi, M. Minge, A° . Skjæveland, S. Nikolaev, K. Jakobsen, and J. Pawlowski, "Phylogenomics Reshuffles the Eukaryotic Supergroups,": PLoS ONE, vol. 2, no. 8, 2007.
-
(2007)
PLoS ONE
, vol.2
, Issue.8
-
-
Burki, F.1
Shalchian-Tabrizi, K.2
Minge, M.3
Skjæveland, A.4
Nikolaev, S.5
Jakobsen, K.6
Pawlowski, J.7
-
32
-
-
57149096433
-
Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures
-
A. Stamatakis and M. Ott, "Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures.": Phil. Trans. R. Soc. series B, Biol. Sci., vol. 363, pp. 3977-3984, 2008.
-
(2008)
Phil. Trans. R. Soc. series B, Biol. Sci.
, vol.363
, pp. 3977-3984
-
-
Stamatakis, A.1
Ott, M.2
-
33
-
-
50249100595
-
A rapid bootstrap algorithm for the raxml web servers
-
A. Stamatakis, P. Hoover, and J. Rougemont, "A Rapid Bootstrap Algorithm for the RAxML Web Servers,": Syst. Biol., vol. 57, no. 5, pp. 758-771, 2008.
-
(2008)
Syst. Biol.
, vol.57
, Issue.5
, pp. 758-771
-
-
Stamatakis, A.1
Hoover, P.2
Rougemont, J.3
-
34
-
-
33646532283
-
Initial experiences porting a bioinformatics application to a graphics processo
-
M. Charalambous, P. Trancoso, and A. Stamatakis, "Initial Experiences Porting a Bioinformatics Application to a Graphics Processor,": In Proc. of the 10th Panhellenic Conference on Informatics (PCI 2005), 2005, pp. 415-425.
-
(2005)
Proc. of the 10th Panhellenic Conference on Informatics (PCI 2005)
, pp. 2005
-
-
Charalambous, M.1
Trancoso, P.2
Stamatakis, A.3
-
35
-
-
70449983022
-
Exploring FPGAs for accelerating the phylogenetic likelihood function
-
accepted for publication
-
N. Alachiotis, E. Sotiriades, A. Dollas, and A. Stamatakis, "Exploring FPGAs for Accelerating the Phylogenetic Likelihood Function,": In Proc. of HICOMB2009, 2009, accepted for publication.
-
(2009)
Proc. of HICOMB2009
-
-
Alachiotis, N.1
Sotiriades, E.2
Dollas, A.3
Stamatakis, A.4
-
36
-
-
48849087982
-
Large-scale phylogenetic analysis on current HPC architectures
-
M. Ott, J. Zola, S. Aluru, A. Johnson, D. Janies, and A. Stamatakis, "Large-scale Phylogenetic Analysis on Current HPC Architectures,": Scientific Programming, vol. 16, no. 2-3, pp. 255-270, 2008.
-
(2008)
Scientific Programming
, vol.16
, Issue.2-3
, pp. 255-270
-
-
Ott, M.1
Zola, J.2
Aluru, S.3
Johnson, A.4
Janies, D.5
Stamatakis, A.6
-
37
-
-
34548754973
-
Building the tree of life on terascale systems
-
X. Feng, K. Cameron, C. Sosa, and B. Smith, "Building the Tree of Life on Terascale Systems,": In Proc. of International Parallel and Distributed Processing Symposium (IPDPS2007), 2007.
-
(2007)
Proc. of International Parallel and Distributed Processing Symposium (IPDPS2007)
-
-
Feng, X.1
Cameron, K.2
Sosa, C.3
Smith, B.4
-
38
-
-
0028064845
-
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites
-
Z. Yang, "Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites,": J. Mol. Evol., vol. 39, pp. 306-314, 1994.
-
(1994)
J. Mol. Evol.
, vol.39
, pp. 306-314
-
-
Yang, Z.1
-
40
-
-
0030928378
-
Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
-
A. Rambaut and N. Grass, "Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees,": Bioinformatics, vol. 13, no. 3, pp. 235-238, 1997.
-
(1997)
Bioinformatics
, vol.13
, Issue.3
, pp. 235-238
-
-
Rambaut, A.1
Grass, N.2
|