-
1
-
-
33745256005
-
Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative
-
Anisimova, M., and O. Gascuel. 2006. Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst. Biol. 55:539-552.
-
(2006)
Syst. Biol
, vol.55
, pp. 539-552
-
-
Anisimova, M.1
Gascuel, O.2
-
2
-
-
34748917568
-
Dynamic multigrain parallelization on the cell broadband engine
-
San Diego, California
-
Blagojevic, F., D. S. Nikolopoulos, A. Stamatakis, and C. D. Antonopoulos. 2007. Dynamic multigrain parallelization on the cell broadband engine. Pages 90-100 in Proceedings of the 12th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. San Diego, California.
-
(2007)
Proceedings of the 12th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming
, pp. 90-100
-
-
Blagojevic, F.1
Nikolopoulos, D.S.2
Stamatakis, A.3
Antonopoulos, C.D.4
-
3
-
-
33646532283
-
Initial experiences porting a bioinformatics application to a graphics processor
-
Charalambous, M., P. Trancoso, and A. Stamatakis. 2005. Initial experiences porting a bioinformatics application to a graphics processor. LNCS 3746:415-425.
-
(2005)
LNCS
, vol.3746
, pp. 415-425
-
-
Charalambous, M.1
Trancoso, P.2
Stamatakis, A.3
-
4
-
-
29144484019
-
Maximum likelihood of evolutionary trees: Hardness and approximation
-
Chor, B., and T. Tuller. 2005. Maximum likelihood of evolutionary trees: Hardness and approximation. Bioinformatics 21:97-106.
-
(2005)
Bioinformatics
, vol.21
, pp. 97-106
-
-
Chor, B.1
Tuller, T.2
-
5
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
DeSantis, T. Z., P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, and G. L. Andersen. 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Env. Microbiol. 72:5069-5072.
-
(2006)
Appl. Env. Microbiol
, vol.72
, pp. 5069-5072
-
-
DeSantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
Rojas, M.4
Brodie, E.L.5
Keller, K.6
Huber, T.7
Dalevi, D.8
Hu, P.9
Andersen, G.L.10
-
6
-
-
42149157760
-
Broad phylogenomic sampling improves resolution of the animal tree of life
-
Dunn, C. W., A. Hejnol, D. Q. Matus, K. Pang, W. E. Browne, S. A. Smith, E. Seaver, G. W. Rouse, M. Obst, G. D. Edgecombe, M. V. Sorensen, S. H. D. Haddock, A. Schmidt-Rhaesa, A. Okusu, R. M. Kristensen, W. C. Wheeler, M. Q. Martindale, and G. Giribet. 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749.
-
(2008)
Nature
, vol.452
, pp. 745-749
-
-
Dunn, C.W.1
Hejnol, A.2
Matus, D.Q.3
Pang, K.4
Browne, W.E.5
Smith, S.A.6
Seaver, E.7
Rouse, G.W.8
Obst, M.9
Edgecombe, G.D.10
Sorensen, M.V.11
Haddock, S.H.D.12
Schmidt-Rhaesa, A.13
Okusu, A.14
Kristensen, R.M.15
Wheeler, W.C.16
Martindale, M.Q.17
Giribet, G.18
-
7
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:368-376.
-
(1981)
J. Mol. Evol
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
8
-
-
0000461280
-
Confidence limits on phylogenies: An approach using the bootstrap
-
Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
-
(1985)
Evolution
, vol.39
, pp. 783-791
-
-
Felsenstein, J.1
-
9
-
-
33746361541
-
PHY.FI: Fast and easy online creation and manipulation of phylogeny color figures
-
Fredslund, J. 2006. PHY.FI: Fast and easy online creation and manipulation of phylogeny color figures. BMC Bioinformatics 7:315.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 315
-
-
Fredslund, J.1
-
10
-
-
0034351387
-
Likelihood-based tests of topologies in phylogenetics
-
Goldman, N., J. P. Anderson, and A. G. Rodrigo. 2000. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49:652-670.
-
(2000)
Syst. Biol
, vol.49
, pp. 652-670
-
-
Goldman, N.1
Anderson, J.P.2
Rodrigo, A.G.3
-
11
-
-
53849128475
-
-
Grimm, G. W., S. S. Renner, A. Stamatakis, and V. Hemleben. 2006. A nuclear ribosomal DNA phylogeny of acer inferred with maximum likelihood, splits graphs, and motif analyses of 606 sequences. Evol. Bioinformatics Online 2:279-294.
-
Grimm, G. W., S. S. Renner, A. Stamatakis, and V. Hemleben. 2006. A nuclear ribosomal DNA phylogeny of acer inferred with maximum likelihood, splits graphs, and motif analyses of 606 sequences. Evol. Bioinformatics Online 2:279-294.
-
-
-
-
12
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
Guindon, S., and O. Gascuel. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
-
(2003)
Syst. Biol
, vol.52
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
13
-
-
23144433822
-
PHYML online - A Web server for fast maximum likelihood-based phylogenetic inference
-
Guindon, S., F. Lethiec, P. Duroux, and O. Gascuel. 2005. PHYML online - A Web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res. 33:557-559.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 557-559
-
-
Guindon, S.1
Lethiec, F.2
Duroux, P.3
Gascuel, O.4
-
14
-
-
22844442543
-
Analysis and visualization of tree space
-
Hillis, D. M., T. A. Heath, and K. S. John. 2005. Analysis and visualization of tree space. Syst. Biol. 54:471-482.
-
(2005)
Syst. Biol
, vol.54
, pp. 471-482
-
-
Hillis, D.M.1
Heath, T.A.2
John, K.S.3
-
15
-
-
28944447963
-
Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood
-
Hordijk, W., and O. Gascuel. 2005. Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood. Bioinformatics 21:4338-4347.
-
(2005)
Bioinformatics
, vol.21
, pp. 4338-4347
-
-
Hordijk, W.1
Gascuel, O.2
-
16
-
-
13444259388
-
Treefinder: A powerful graphical analysis environment for molecular phylogenetics
-
Jobb, G., A. von Haeseler, and K. Strimmer. 2004. Treefinder: A powerful graphical analysis environment for molecular phylogenetics. BMC Evol. Biol. 4:18.
-
(2004)
BMC Evol. Biol
, vol.4
, pp. 18
-
-
Jobb, G.1
von Haeseler, A.2
Strimmer, K.3
-
17
-
-
34547583680
-
MultiPhyl: A high-throughput phylogenomics Webserver using distributed computing
-
Keane, T. M., T. J. Naughton, and J. O. McInerney. 2007. MultiPhyl: A high-throughput phylogenomics Webserver using distributed computing. Nucleic Acids Res. 35:W33-W37.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Keane, T.M.1
Naughton, T.J.2
McInerney, J.O.3
-
18
-
-
16344387501
-
DPRml: Distributed phylogeny reconstruction by maximum likelihood
-
Keane, T. M., T. J. Naughton, S. A. A. Travers, J. O. McInerney, and G. P. McCormack. 2005. DPRml: Distributed phylogeny reconstruction by maximum likelihood. Bioinformatics 21:969-974.
-
(2005)
Bioinformatics
, vol.21
, pp. 969-974
-
-
Keane, T.M.1
Naughton, T.J.2
Travers, S.A.A.3
McInerney, J.O.4
McCormack, G.P.5
-
19
-
-
34547803149
-
Phylogenetic supermatrix analysis of Genbank sequences from 2228 papilionoid legumes
-
McMahon, M. M., and M. J. Sanderson. 2006. Phylogenetic supermatrix analysis of Genbank sequences from 2228 papilionoid legumes. Syst. Biol. 55:818-836.
-
(2006)
Syst. Biol
, vol.55
, pp. 818-836
-
-
McMahon, M.M.1
Sanderson, M.J.2
-
20
-
-
27144503359
-
PIQPNNI: Parallel reconstruction of large maximum likelihood phylogenies
-
Minh, B. Q., L. S. Vinh, A. von Haeseler, and H. A. Schmidt. 2005. PIQPNNI: Parallel reconstruction of large maximum likelihood phylogenies. Bioinformatics 21:3794-3796.
-
(2005)
Bioinformatics
, vol.21
, pp. 3794-3796
-
-
Minh, B.Q.1
Vinh, L.S.2
von Haeseler, A.3
Schmidt, H.A.4
-
21
-
-
14044249689
-
Towards a discipline of experimental algorithmics
-
M. H. Goldwasser, D. Johnson, and C. McGeoch, eds, of DIMACS Monographs. American Mathematical Society. Providence, Rhode Island
-
Moret, B. M. E. 2002. Towards a discipline of experimental algorithmics. Pages 197-213 in Data structures, near neighbor searches, and methodology: Fifth and Sixth DIMACS Implementation Challenges (M. H. Goldwasser, D. Johnson, and C. McGeoch, eds.), volume 59 of DIMACS Monographs. American Mathematical Society. Providence, Rhode Island.
-
(2002)
Data structures, near neighbor searches, and methodology: Fifth and Sixth DIMACS Implementation Challenges
, vol.59
, pp. 197-213
-
-
Moret, B.M.E.1
-
22
-
-
39549109362
-
Increasing the efficiency of searches for the maximum likelihood tree in a phylogenetic analysis of up to 150 nucleotide sequences
-
Morrison, D. A. 2007. Increasing the efficiency of searches for the maximum likelihood tree in a phylogenetic analysis of up to 150 nucleotide sequences. Syst. Biol. 56:988-1010.
-
(2007)
Syst. Biol
, vol.56
, pp. 988-1010
-
-
Morrison, D.A.1
-
23
-
-
56849127431
-
Large-scale maximum likelihood-based phylogenetic analysis on the IBM blue-Gene/L
-
Reno, Nevada, USA
-
Ott, M., J. Zola, S. Aluru, and A. Stamatakis. 2007. Large-scale maximum likelihood-based phylogenetic analysis on the IBM blue-Gene/L. In On-Line Proceedings of IEEE/ACM Supercomputing Conference 2007. Reno, Nevada, USA.
-
(2007)
On-Line Proceedings of IEEE/ACM Supercomputing Conference
-
-
Ott, M.1
Zola, J.2
Aluru, S.3
Stamatakis, A.4
-
24
-
-
47749153850
-
Does choice in model selection affect maximum likelihood analysis?
-
Ripplinger, J., and J. Sullivan. 2008. Does choice in model selection affect maximum likelihood analysis? Syst. Biol. 57:76-85.
-
(2008)
Syst. Biol
, vol.57
, pp. 76-85
-
-
Ripplinger, J.1
Sullivan, J.2
-
25
-
-
0039348203
-
Comparison of weighted labelled trees
-
Robinson, D. F., and L. R. Foulds. 1979. Comparison of weighted labelled trees. Lecture Notes Math. 748:119-126.
-
(1979)
Lecture Notes Math
, vol.748
, pp. 119-126
-
-
Robinson, D.F.1
Foulds, L.R.2
-
26
-
-
0019424782
-
Comparison of phylogenetic trees
-
Robinson, D. F., and L. R. Foulds. 1981. Comparison of phylogenetic trees. Math. Biosci. 53:131-147.
-
(1981)
Math. Biosci
, vol.53
, pp. 131-147
-
-
Robinson, D.F.1
Foulds, L.R.2
-
27
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
Ronquist, F., and J. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
-
(2003)
Bioinformatics
, vol.19
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.2
-
28
-
-
0036205377
-
TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
-
Schmidt, H. A., K. Strimmer, M. Vingron, and A. von Haeseler. 2002. TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.
-
(2002)
Bioinformatics
, vol.18
, pp. 502-504
-
-
Schmidt, H.A.1
Strimmer, K.2
Vingron, M.3
von Haeseler, A.4
-
30
-
-
33750403801
-
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis, A. 2006b. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
-
(2006)
Bioinformatics
, vol.22
, pp. 2688-2690
-
-
Stamatakis, A.1
-
31
-
-
34548446701
-
Exploring new search algorithms and hardware for phylogenetics: RAxML meets the IBM cell
-
Stamatakis, A., F. Blagojevic, C. D. Antonopoulos, and D. S. Nikolopoulos. 2007. Exploring new search algorithms and hardware for phylogenetics: RAxML meets the IBM cell. J. VLSI Sig. Proc. Sys. 48:271-286.
-
(2007)
J. VLSI Sig. Proc. Sys
, vol.48
, pp. 271-286
-
-
Stamatakis, A.1
Blagojevic, F.2
Antonopoulos, C.D.3
Nikolopoulos, D.S.4
-
32
-
-
14644397888
-
RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees
-
Stamatakis, A., T. Ludwig, and H. Meier. 2005a. RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21:456-463.
-
(2005)
Bioinformatics
, vol.21
, pp. 456-463
-
-
Stamatakis, A.1
Ludwig, T.2
Meier, H.3
-
33
-
-
26844521242
-
RAxML-OMP: An efficient program for phylogenetic inference on SMPs
-
Stamatakis, A., M. Ott, and T. Ludwig. 2005b. RAxML-OMP: An efficient program for phylogenetic inference on SMPs. LNCS 3606:288-302.
-
(2005)
LNCS
, vol.3606
, pp. 288-302
-
-
Stamatakis, A.1
Ott, M.2
Ludwig, T.3
-
34
-
-
0029836454
-
Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies
-
Strimmer, K. and A. von Haeseler. 1996. Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969.
-
(1996)
Mol. Biol. Evol
, vol.13
, pp. 964-969
-
-
Strimmer, K.1
von Haeseler, A.2
-
35
-
-
53849121905
-
-
Swofford, D. L. 2002. PAUP*: Phylogenetic analysis using parsimony *and other methods, Version 4.0b10. Sinauer Associates, Sunderland, Massachusetts
-
Swofford, D. L. 2002. PAUP*: Phylogenetic analysis using parsimony (*and other methods). Version 4.0b10. Sinauer Associates, Sunderland, Massachusetts.
-
-
-
-
36
-
-
34547585235
-
Phylemon: A suite of Web tools for molecular evolution, phylogenetics and phylogenomics
-
Tarraga, J., I. Medina, L. Arbiza, J. Huerta-Cepas, T. Gabaldon, J. Dopazo, and H. Dopazo. 2007. Phylemon: A suite of Web tools for molecular evolution, phylogenetics and phylogenomics. Nucleic Acids Res. 35:W38.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Tarraga, J.1
Medina, I.2
Arbiza, L.3
Huerta-Cepas, J.4
Gabaldon, T.5
Dopazo, J.6
Dopazo, H.7
-
37
-
-
84879540883
-
PhyNav: A novel approach to reconstruct large phylogenies
-
Heidelberg/New York
-
Vinh, L. S., H. A. Schmidt, and A. von Haeseler. 2005. PhyNav: A novel approach to reconstruct large phylogenies. Pages 386-393 in Classification, the Ubiquitous Challenge. (Proceedings of the 28th Annual Conference of the GfKl 2004). Studies in classification, data analysis, and knowledge organization Springer, Heidelberg/New York.
-
(2005)
Classification, the Ubiquitous Challenge. (Proceedings of the 28th Annual Conference of the GfKl 2004). Studies in classification, data analysis, and knowledge organization Springer
, pp. 386-393
-
-
Vinh, L.S.1
Schmidt, H.A.2
von Haeseler, A.3
-
38
-
-
0142089657
-
Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data
-
Waddell, P. J., H. Kishino, and R. Ota. 2002. Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data. Gen. Informatic 13:82-92.
-
(2002)
Gen. Informatic
, vol.13
, pp. 82-92
-
-
Waddell, P.J.1
Kishino, H.2
Ota, R.3
-
39
-
-
34548633617
-
New approaches to phylogenetic tree search and their application to large numbers of protein alignments
-
Whelan, S. 2007. New approaches to phylogenetic tree search and their application to large numbers of protein alignments. Syst. Biol. 56:727-740.
-
(2007)
Syst. Biol
, vol.56
, pp. 727-740
-
-
Whelan, S.1
-
40
-
-
1342320051
-
The memory gap and the future of high performance memories
-
Wilkes, M. 2001. The memory gap and the future of high performance memories. ACM SIGARCH Computer Architecture News 29:2-7.
-
(2001)
ACM SIGARCH Computer Architecture News
, vol.29
, pp. 2-7
-
-
Wilkes, M.1
|