-
1
-
-
17744398025
-
More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy
-
Rokas, A. and Carroll, S.B., More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy, Mol. Biol. Evol., 22, 1337, 2005.
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 1337
-
-
Rokas, A.1
Carroll, S.B.2
-
2
-
-
19944417239
-
Supertree construction in the genomic age, in Molecular Evolution: Producing the Biochemical Data
-
part B, Zimmer, E.A. and Roalson, E., Eds., Elsevier, Amsterdam
-
Bininda-Emonds, O.R.P., Supertree construction in the genomic age, in Molecular Evolution: Producing the Biochemical Data, part B, Zimmer, E.A. and Roalson, E., Eds., Methods in Enzymology, Vol. 395, Elsevier, Amsterdam, 2005, 745.
-
(2005)
Methods in Enzymology
, vol.395
, pp. 745
-
-
Bininda-Emonds, O.R.P.1
-
3
-
-
0042695888
-
The challenge of constructing large phylogenetic trees
-
Sanderson, M.J. and Driskell, A.C., The challenge of constructing large phylogenetic trees, Trends Pl. Sci., 8, 374, 2003.
-
(2003)
Trends Pl. Sci.
, vol.8
, pp. 374
-
-
Sanderson, M.J.1
Driskell, A.C.2
-
4
-
-
11144357823
-
Taxonomy as a fundamental discipline
-
Wilson, E.O., Taxonomy as a fundamental discipline, Philos. Trans. R. Soc. Lond. B, 359, 739, 2004.
-
(2004)
Philos. Trans. R. Soc. Lond. B
, vol.359
, pp. 739
-
-
Wilson, E.O.1
-
5
-
-
84959792503
-
The number of evolutionary trees
-
Felsenstein, J., The number of evolutionary trees, Syst. Zool., 27, 27, 1978.
-
(1978)
Syst. Zool.
, vol.27
, pp. 27
-
-
Felsenstein, J.1
-
6
-
-
10244219919
-
QuickJoin: Fast neighbour-joining tree reconstruction
-
Mailund, T. and Pedersen, C.N., QuickJoin: fast neighbour-joining tree reconstruction, Bioinformatics, 20, 3261, 2004.
-
(2004)
Bioinformatics
, vol.20
, pp. 3261
-
-
Mailund, T.1
Pedersen, C.N.2
-
7
-
-
35048835879
-
Parallel inference of a 10,000-taxon phylogeny with maximum likelihood
-
Springer Verlag
-
Stamatakis, A., Parallel inference of a 10,000-taxon phylogeny with maximum likelihood, in Proceedings of 10th International Euro-Par Conference (Euro-Par 2004), Springer Verlag, 2004, 997.
-
(2004)
Proceedings of 10th International Euro-Par Conference (Euro-Par 2004)
, pp. 997
-
-
Stamatakis, A.1
-
9
-
-
14044251530
-
Rec-I-DCM3: A fast algorithmic technique for reconstructing large phylogenetic trees
-
IEEE Computer Society Press, Stanford, California
-
Roshan, U. et al., Rec-I-DCM3: a fast algorithmic technique for reconstructing large phylogenetic trees, in Proceedings of the IEEE Computational Systems Bioinformatics conference (CSB), IEEE Computer Society Press, Stanford, California, 2004.
-
(2004)
Proceedings of the IEEE Computational Systems Bioinformatics conference (CSB)
-
-
Roshan, U.1
-
11
-
-
19044382857
-
Towards building the tree of life: A simulation study for all angiosperm taxa
-
Salamin, N., Hodkinson, T.R., and Savolainen, V., Towards building the tree of life: a simulation study for all angiosperm taxa, Syst. Biol., 54, 183, 2005.
-
(2005)
Syst. Biol.
, vol.54
, pp. 183
-
-
Salamin, N.1
Hodkinson, T.R.2
Savolainen, V.3
-
12
-
-
0029834661
-
Inferring complex phylogenies
-
Hillis, D.M., Inferring complex phylogenies, Nature, 383, 130, 1996.
-
(1996)
Nature
, vol.383
, pp. 130
-
-
Hillis, D.M.1
-
13
-
-
0035222013
-
Scaling of accuracy in extremely large phylogenetic trees
-
Altman, R.B. et al., Eds., World Scientific Publishing Company, River Edge, NJ
-
Bininda-Emonds, O.R.P. et al., Scaling of accuracy in extremely large phylogenetic trees, in Pacific Symposium on Biocomputing 2001, Altman, R.B. et al., Eds., World Scientific Publishing Company, River Edge, NJ, 2000, 547.
-
(2000)
Pacific Symposium on Biocomputing 2001
, pp. 547
-
-
Bininda-Emonds, O.R.P.1
-
14
-
-
0033480324
-
A few logs suffice to build (almost) all trees (I)
-
Erdös, P.L. et al., A few logs suffice to build (almost) all trees (I), Random Struc. Alg., 14, 153, 1999.
-
(1999)
Random Struc. Alg.
, vol.14
, pp. 153
-
-
Erdös, P.L.1
-
15
-
-
0001860411
-
A few logs suffice to build (almost) all trees: Part II
-
Erdös, P.L. et al., A few logs suffice to build (almost) all trees: part II, Theoret. Comput. Sci., 221, 77, 1999.
-
(1999)
Theoret. Comput. Sci.
, vol.221
, pp. 77
-
-
Erdös, P.L.1
-
16
-
-
12044255023
-
Success of phylogenetic methods in the four-taxon case
-
Huelsenbeck, J.P. and Hillis, D.M., Success of phylogenetic methods in the four-taxon case, Syst. Biol., 42, 247, 1993.
-
(1993)
Syst. Biol.
, vol.42
, pp. 247
-
-
Huelsenbeck, J.P.1
Hillis, D.M.2
-
17
-
-
20444491634
-
A review of long-branch attraction
-
Bergsten, J., A review of long-branch attraction, Cladistics, 21, 163, 2005.
-
(2005)
Cladistics
, vol.21
, pp. 163
-
-
Bergsten, J.1
-
18
-
-
0032023889
-
Taxonomic sampling, phylogenetic accuracy, and investigator bias
-
Hillis, D.M., Taxonomic sampling, phylogenetic accuracy, and investigator bias, Syst. Biol., 47, 3, 1998.
-
(1998)
Syst. Biol.
, vol.47
, pp. 3
-
-
Hillis, D.M.1
-
19
-
-
0036699885
-
Increased taxon sampling is advantageous for phylogenetic inference
-
Pollock, D.D. et al., Increased taxon sampling is advantageous for phylogenetic inference, Syst. Biol., 51, 664, 2002.
-
(2002)
Syst. Biol.
, vol.51
, pp. 664
-
-
Pollock, D.D.1
-
20
-
-
0032025857
-
Is it better to add taxa or characters to a difficult phylogenetic problem?
-
Graybeal, A., Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol., 47, 9, 1998.
-
(1998)
Syst. Biol.
, vol.47
, pp. 9
-
-
Graybeal, A.1
-
21
-
-
0035845536
-
Incomplete taxon sampling is not a problem for phylogenetic inference
-
Rosenberg, M.S. and Kumar, S., Incomplete taxon sampling is not a problem for phylogenetic inference, Proc. Natl. Acad. Sci. USA, 98, 10751, 2001.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 10751
-
-
Rosenberg, M.S.1
Kumar, S.2
-
22
-
-
0029836454
-
Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies
-
Strimmer, K. and von Haeseler, A., Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies, Mol. Biol. Evol., 13, 964, 1996.
-
(1996)
Mol. Biol. Evol.
, vol.13
, pp. 964
-
-
Strimmer, K.1
von Haeseler, A.2
-
23
-
-
0032746022
-
Disk-covering, a fast-converging method for phylogenetic tree reconstruction
-
Huson, D.H., Nettles, S.M., and Warnow, T.J., Disk-covering, a fast-converging method for phylogenetic tree reconstruction, J. Comput. Biol., 6, 369, 1999.
-
(1999)
J. Comput. Biol.
, vol.6
, pp. 369
-
-
Huson, D.H.1
Nettles, S.M.2
Warnow, T.J.3
-
24
-
-
0033289315
-
Solving large scale phylogenetic problems using DCM2
-
Lengauer, T. et al., Eds., AAAI Press, Menlo Park, California
-
Huson, D.H., Vawter, L., and Warnow, T.J., Solving large scale phylogenetic problems using DCM2, in Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, Lengauer, T. et al., Eds., AAAI Press, Menlo Park, California, 1999, 118.
-
(1999)
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
, pp. 118
-
-
Huson, D.H.1
Vawter, L.2
Warnow, T.J.3
-
25
-
-
0037314098
-
Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
-
Sanderson, M.J., r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock, Bioinformatics, 19, 301, 2003.
-
(2003)
Bioinformatics
, vol.19
, pp. 301
-
-
Sanderson, M.J.1
-
26
-
-
0030928378
-
Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
-
Rambaut, A. and Grassly, N.C., Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees, Comput. Appl. Biosci., 13, 235, 1997.
-
(1997)
Comput. Appl. Biosci.
, vol.13
, pp. 235
-
-
Rambaut, A.1
Grassly, N.C.2
-
27
-
-
0001336205
-
Phylogenetic inference
-
Hillis, D.M., Moritz, C., and Mable, B.K., Eds., Sinauer Associates, Sunderland, Massachusetts
-
Swofford, D.L. et al., Phylogenetic inference, in Molecular Systematics, Hillis, D.M., Moritz, C., and Mable, B.K., Eds., Sinauer Associates, Sunderland, Massachusetts, 1996, 407.
-
(1996)
Molecular Systematics
, pp. 407
-
-
Swofford, D.L.1
-
28
-
-
2442489795
-
Performance of supertree methods on various data set decompositions
-
Bininda-Emonds, O.R.P., Ed., Kluwer Academic, Dordrecht, Netherlands
-
Roshan, U. et al., Performance of supertree methods on various data set decompositions, in Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, Bininda-Emonds, O.R.P., Ed., Kluwer Academic, Dordrecht, Netherlands, 2004, 301.
-
(2004)
Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life
, pp. 301
-
-
Roshan, U.1
-
29
-
-
12444334567
-
New, fast and accurate heuristics for inference of large phylogenetic trees
-
IEEE Computer Society, Santa Fe, New Mexico
-
Stamatakis, A., Ludwig, T., and Meier, H., New, fast and accurate heuristics for inference of large phylogenetic trees, in Proceedings of 18th IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS2004), High Performance Computational Biology Workshop, IEEE Computer Society, Santa Fe, New Mexico, 2004.
-
(2004)
Proceedings of 18th IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS2004), High Performance Computational Biology Workshop
-
-
Stamatakis, A.1
Ludwig, T.2
Meier, H.3
-
31
-
-
0033504552
-
The parsimony ratchet, a new method for rapid parsimony analysis
-
Nixon, K.C., The parsimony ratchet, a new method for rapid parsimony analysis, Cladistics, 15, 407, 1999.
-
(1999)
Cladistics
, vol.15
, pp. 407
-
-
Nixon, K.C.1
-
32
-
-
0036857358
-
Bateman, A., and Durbin, R., QuickTree: Building huge neighbour-joining trees of protein sequences
-
Howe, K., Bateman, A., and Durbin, R., QuickTree: building huge neighbour-joining trees of protein sequences, Bioinformatics, 18, 1546, 2002.
-
(2002)
Bioinformatics
, vol.18
, pp. 1546
-
-
Howe, K.1
-
33
-
-
14644397888
-
RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees
-
Stamatakis, A., Ludwig, T., and Meier, H., RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees, Bioinformatics, 21, 456, 2005.
-
(2005)
Bioinformatics
, vol.21
, pp. 456
-
-
Stamatakis, A.1
Ludwig, T.2
Meier, H.3
-
34
-
-
18244389982
-
AxML: A fast program for sequential and parallel phylogenetic tree calculations based on the maximum likelihood method
-
Stamatakis, A.P. et al., AxML: a fast program for sequential and parallel phylogenetic tree calculations based on the maximum likelihood method, Proc. IEEE Comput. Soc. Bioinform. Conf., 1, 21, 2002.
-
(2002)
Proc. IEEE Comput. Soc. Bioinform. Conf.
, vol.1
, pp. 21
-
-
Stamatakis, A.P.1
-
35
-
-
84959758123
-
Congruence between morphometric and allozyme data for Menidia species: A reappraisal
-
Colless, D.H., Congruence between morphometric and allozyme data for Menidia species: a reappraisal, Syst. Zool., 29, 288, 1980.
-
(1980)
Syst. Zool.
, vol.29
, pp. 288
-
-
Colless, D.H.1
-
36
-
-
0005745748
-
Predictivity and stability in classifications: Some comments on recent studies
-
Colless, D.H., Predictivity and stability in classifications: some comments on recent studies, Syst. Zool., 30, 325, 1981.
-
(1981)
Syst. Zool.
, vol.30
, pp. 325
-
-
Colless, D.H.1
-
37
-
-
0019424782
-
Comparison of phylogenetic trees
-
Robinson, D.F. and Foulds, L.R., Comparison of phylogenetic trees, Math. Biosci., 53, 131, 1981.
-
(1981)
Math. Biosci.
, vol.53
, pp. 131
-
-
Robinson, D.F.1
Foulds, L.R.2
-
38
-
-
52449147252
-
The complexity of reconstructing trees from qualitative characters and subtrees
-
Steel, M., The complexity of reconstructing trees from qualitative characters and subtrees, J. Classif., 9, 91, 1992.
-
(1992)
J. Classif.
, vol.9
, pp. 91
-
-
Steel, M.1
-
39
-
-
0242365676
-
Genome-scale approaches to resolving incongruence in molecular phylogenies
-
Rokas, A. et al., Genome-scale approaches to resolving incongruence in molecular phylogenies, Nature, 425, 798, 2003.
-
(2003)
Nature
, vol.425
, pp. 798
-
-
Rokas, A.1
-
40
-
-
0028362880
-
Application and accuracy of molecular phylogenies
-
Hillis, D.M., Huelsenbeck, J.P., and Cunningham, C.W., Application and accuracy of molecular phylogenies, Science, 264, 671, 1994.
-
(1994)
Science
, vol.264
, pp. 671
-
-
Hillis, D.M.1
Huelsenbeck, J.P.2
Cunningham, C.W.3
-
41
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
Guindon, S. and Gascuel, O., A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, Syst. Biol., 52, 696, 2003.
-
(2003)
Syst. Biol.
, vol.52
, pp. 696
-
-
Guindon, S.1
Gascuel, O.2
-
42
-
-
0032766033
-
Multiple local maxima for likelihoods of phylogenetic trees: A simulation study
-
Rogers, J.S. and Swofford, D.L., Multiple local maxima for likelihoods of phylogenetic trees: a simulation study, Mol. Biol. Evol., 16, 1079, 1999.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 1079
-
-
Rogers, J.S.1
Swofford, D.L.2
-
43
-
-
0033499153
-
Analyzing large data sets in reasonable times: Solutions for composite optima
-
Goloboff, P.A., Analyzing large data sets in reasonable times: solutions for composite optima, Cladistics, 15, 415, 1999.
-
(1999)
Cladistics
, vol.15
, pp. 415
-
-
Goloboff, P.A.1
-
44
-
-
0038781911
-
Assessing internal support with large phylogenetic DNA matrices
-
Salamin, N. et al., Assessing internal support with large phylogenetic DNA matrices, Mol. Phylogenet. Evol., 27, 528, 2003.
-
(2003)
Mol. Phylogenet. Evol.
, vol.27
, pp. 528
-
-
Salamin, N.1
-
45
-
-
0028069573
-
Accuracies of the simple methods for estimating the bootstrap probability of a maximum-likelihood tree
-
Hasegawa, M. and Kishino, H., Accuracies of the simple methods for estimating the bootstrap probability of a maximum-likelihood tree, Mol. Biol. Evol., 11, 142, 1994.
-
(1994)
Mol. Biol. Evol.
, vol.11
, pp. 142
-
-
Hasegawa, M.1
Kishino, H.2
-
46
-
-
0025181359
-
Maximum likelihood inference of protein phylogeny and the origin of chloroplasts
-
Kishino, H., Miyata, T., and Hasegawa, M., Maximum likelihood inference of protein phylogeny and the origin of chloroplasts, J. Mol. Evol., 31, 151, 1990.
-
(1990)
J. Mol. Evol.
, vol.31
, pp. 151
-
-
Kishino, H.1
Miyata, T.2
Hasegawa, M.3
-
47
-
-
0142089657
-
Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data
-
Lathrop, R. et al., Eds., Universal Academy Press, Tokyo
-
Waddell, P.J., Kishino, H., and Ota, R., Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data, in Genome Informatics 2002, Lathrop, R. et al., Eds., Universal Academy Press, Tokyo, 2002, 82.
-
(2002)
Genome Informatics 2002
, pp. 82
-
-
Waddell, P.J.1
Kishino, H.2
Ota, R.3
-
48
-
-
0030315308
-
General inconsistency conditions for maximum parsimony: Effects of branch lengths and increasing numbers of taxa
-
Kim, J., General inconsistency conditions for maximum parsimony: effects of branch lengths and increasing numbers of taxa, Syst. Biol., 45, 363, 1996.
-
(1996)
Syst. Biol.
, vol.45
, pp. 363
-
-
Kim, J.1
-
49
-
-
3242801484
-
IQPNNI: Moving fast through tree space and stopping in time
-
le Vinh, S. and Von Haeseler, A., IQPNNI: moving fast through tree space and stopping in time, Mol. Biol. Evol., 21, 1565, 2004.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 1565
-
-
Le Vinh, S.1
Von Haeseler, A.2
-
50
-
-
33646388245
-
Parallel divide-and-conquer phylogeny reconstruction by maximum likelihood
-
Dongarra, J. et al., Eds., Springer Verlag, Berlin
-
Du, Z. et al., Parallel divide-and-conquer phylogeny reconstruction by maximum likelihood, in High Performance Computing and Communications: First International Conference, HPCC 2005, Sorrento, Italy, September, 21-23, 2005, Proceedings, Dongarra, J. et al., Eds., Springer Verlag, Berlin, 2005, 776.
-
(2005)
High Performance Computing and Communications: First International Conference, HPCC 2005, Sorrento, Italy, September, 21-23, 2005, Proceedings
, pp. 776
-
-
Du, Z.1
-
51
-
-
0035527411
-
Assessment of the accuracy of matrix representation with parsimony supertree construction
-
Bininda-Emonds, O.R.P. and Sanderson, M.J., Assessment of the accuracy of matrix representation with parsimony supertree construction, Syst. Biol., 50, 565, 2001.
-
(2001)
Syst. Biol.
, vol.50
, pp. 565
-
-
Bininda-Emonds, O.R.P.1
Sanderson, M.J.2
|