-
1
-
-
0033920569
-
Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA
-
Adachi J., Waddell P.J., Martin W., and Hasegawa M. Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. J. Mol. Evol. 50 (2000) 348-358
-
(2000)
J. Mol. Evol.
, vol.50
, pp. 348-358
-
-
Adachi, J.1
Waddell, P.J.2
Martin, W.3
Hasegawa, M.4
-
2
-
-
33846839390
-
Bayesian estimation of concordance among gene trees
-
Ané C., Larget B., Baum D.A., Smith S.D., and Rokas A. Bayesian estimation of concordance among gene trees. Mol. Biol. Evol. 24 (2007) 412-426
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 412-426
-
-
Ané, C.1
Larget, B.2
Baum, D.A.3
Smith, S.D.4
Rokas, A.5
-
3
-
-
33745256005
-
Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative
-
Anisimova M., and Gascuel O. Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst. Biol. 55 (2006) 539-552
-
(2006)
Syst. Biol.
, vol.55
, pp. 539-552
-
-
Anisimova, M.1
Gascuel, O.2
-
4
-
-
2342651581
-
Bayesian gene/species tree reconciliation and orthology analysis using mcmc
-
Arvestad L., Berglund A.-C., Lagergren J., and Sennblad B. Bayesian gene/species tree reconciliation and orthology analysis using mcmc. Bioinformatics 19 (2003) 7-15
-
(2003)
Bioinformatics
, vol.19
, pp. 7-15
-
-
Arvestad, L.1
Berglund, A.-C.2
Lagergren, J.3
Sennblad, B.4
-
6
-
-
0002844544
-
Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees
-
Baum B.R. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41 (1992) 3-10
-
(1992)
Taxon
, vol.41
, pp. 3-10
-
-
Baum, B.R.1
-
7
-
-
33846839295
-
Concordance trees, concordance factors, and the exploration of reticulate genealogy
-
Baum D.A. Concordance trees, concordance factors, and the exploration of reticulate genealogy. Taxon. 56 (2007) 417-426
-
(2007)
Taxon.
, vol.56
, pp. 417-426
-
-
Baum, D.A.1
-
8
-
-
33645568886
-
Phylogenetic identification of lateral genetic transfer events
-
Beiko R.G., and Hamilton N. Phylogenetic identification of lateral genetic transfer events. BMC Evol. Biol. 6 (2006) 15
-
(2006)
BMC Evol. Biol.
, vol.6
, pp. 15
-
-
Beiko, R.G.1
Hamilton, N.2
-
9
-
-
33746433923
-
Optimal gene trees from sequences and species trees using a soft interpretation of parsimony
-
Berglund-Sonnhammer A.C., Steffansson P., Betts M.J., and Liberles D.A. Optimal gene trees from sequences and species trees using a soft interpretation of parsimony. J. Mol. Evol. 63 (2006) 240-250
-
(2006)
J. Mol. Evol.
, vol.63
, pp. 240-250
-
-
Berglund-Sonnhammer, A.C.1
Steffansson, P.2
Betts, M.J.3
Liberles, D.A.4
-
10
-
-
0032148631
-
Properties of matrix representation with parsimony analyses
-
Bininda-Emonds O.R.P., and Bryant H.N. Properties of matrix representation with parsimony analyses. Syst. Biol. 47 (1998) 497-508
-
(1998)
Syst. Biol.
, vol.47
, pp. 497-508
-
-
Bininda-Emonds, O.R.P.1
Bryant, H.N.2
-
11
-
-
0035527411
-
Assessment of the accuracy of matrix representation with parsimony analysis supertree construction
-
Bininda-Emonds O.R.P., and Sanderson M.J. Assessment of the accuracy of matrix representation with parsimony analysis supertree construction. Syst. Biol. 50 (2001) 565-579
-
(2001)
Syst. Biol.
, vol.50
, pp. 565-579
-
-
Bininda-Emonds, O.R.P.1
Sanderson, M.J.2
-
12
-
-
0038325772
-
Testing for phylogenetic signal in comparative data: Behavioral traits are more labile
-
Blomberg S.P., Garland T., and Ives A.R. Testing for phylogenetic signal in comparative data: Behavioral traits are more labile. Evolution 57 (2003) 717-745
-
(2003)
Evolution
, vol.57
, pp. 717-745
-
-
Blomberg, S.P.1
Garland, T.2
Ives, A.R.3
-
14
-
-
0030512416
-
Gene trees, species trees, and systematics: a cladistic perspective
-
Brower A.V.Z., DeSalle R., and Vogler A. Gene trees, species trees, and systematics: a cladistic perspective. Annu. Rev. Ecol. Evol. S 27 (1996) 423-450
-
(1996)
Annu. Rev. Ecol. Evol. S
, vol.27
, pp. 423-450
-
-
Brower, A.V.Z.1
DeSalle, R.2
Vogler, A.3
-
15
-
-
1642519173
-
A classification of consensus methods for phylogenies
-
Janowitz M., Lapointe F.-J., McMorris F.R., Mirkin B., and Roberts F.S. (Eds), American Mathematical Society, Providence, RI
-
Bryant D. A classification of consensus methods for phylogenies. In: Janowitz M., Lapointe F.-J., McMorris F.R., Mirkin B., and Roberts F.S. (Eds). BioConsensus, Center for Discrete Mathematics and Theoretical Computer Science (2003), American Mathematical Society, Providence, RI 163-184
-
(2003)
BioConsensus, Center for Discrete Mathematics and Theoretical Computer Science
, pp. 163-184
-
-
Bryant, D.1
-
16
-
-
33747338447
-
Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (maoricicada dugdale)
-
Buckley T.R., Cordeiro M., Marshall D.C., and Simon C. Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (maoricicada dugdale). Syst. Biol. 55 (2006) 411-425
-
(2006)
Syst. Biol.
, vol.55
, pp. 411-425
-
-
Buckley, T.R.1
Cordeiro, M.2
Marshall, D.C.3
Simon, C.4
-
17
-
-
0031694349
-
Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders
-
Cao Y., Janke A., Waddell P.J., Westerman M., Takenaka O., Murata S., Okada N., Paabo S., and Hasegawa M. Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders. J. Mol. Evol. 47 (1998) 307-322
-
(1998)
J. Mol. Evol.
, vol.47
, pp. 307-322
-
-
Cao, Y.1
Janke, A.2
Waddell, P.J.3
Westerman, M.4
Takenaka, O.5
Murata, S.6
Okada, N.7
Paabo, S.8
Hasegawa, M.9
-
18
-
-
34249700809
-
Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from melanoplus grasshoppers
-
Carstens B.C., and Knowles L.L. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from melanoplus grasshoppers. Syst. Biol. 56 (2007) 400-411
-
(2007)
Syst. Biol.
, vol.56
, pp. 400-411
-
-
Carstens, B.C.1
Knowles, L.L.2
-
20
-
-
34548566074
-
Majority-rule supertrees
-
Cotton J.A., and Wilkinson M. Majority-rule supertrees. Syst. Biol. 56 (2007) 445-452
-
(2007)
Syst. Biol.
, vol.56
, pp. 445-452
-
-
Cotton, J.A.1
Wilkinson, M.2
-
22
-
-
68049093070
-
-
Degnan, J.H., DeGiorgio, M., Bryant, D., Rosenberg, N.A., 2008. Properties of consensus methods for inferring species trees from gene trees. arxiv:/arXiv:0802.2355v1 [q-bio.PE].
-
Degnan, J.H., DeGiorgio, M., Bryant, D., Rosenberg, N.A., 2008. Properties of consensus methods for inferring species trees from gene trees. arxiv:/arXiv:0802.2355v1 [q-bio.PE].
-
-
-
-
23
-
-
33646928341
-
Discordance of species trees with their most likely gene trees
-
Degnan J.H., and Rosenberg N.A. Discordance of species trees with their most likely gene trees. Plos Genet. 2 (2006) 762-768
-
(2006)
Plos Genet.
, vol.2
, pp. 762-768
-
-
Degnan, J.H.1
Rosenberg, N.A.2
-
24
-
-
13244292527
-
Gene tree distributions under the coalescent process
-
Degnan J.H., and Salter L.A. Gene tree distributions under the coalescent process. Evolution 59 (2005) 24-37
-
(2005)
Evolution
, vol.59
, pp. 24-37
-
-
Degnan, J.H.1
Salter, L.A.2
-
25
-
-
0000989175
-
Gene trees and species trees - molecular systematics as one-character taxonomy
-
Doyle J.J. Gene trees and species trees - molecular systematics as one-character taxonomy. Syst. Bot. 17 (1992) 144-163
-
(1992)
Syst. Bot.
, vol.17
, pp. 144-163
-
-
Doyle, J.J.1
-
26
-
-
56549103832
-
Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow
-
Eckert A.J., and Carstens B.C. Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow. Mol. Phylogenet. Evol. 49 (2008) 832-842
-
(2008)
Mol. Phylogenet. Evol.
, vol.49
, pp. 832-842
-
-
Eckert, A.J.1
Carstens, B.C.2
-
27
-
-
58249100073
-
Is a new and general theory of molecular systematics emerging?
-
Edwards S.V. Is a new and general theory of molecular systematics emerging?. Evolution 63 (2009) 1-19
-
(2009)
Evolution
, vol.63
, pp. 1-19
-
-
Edwards, S.V.1
-
28
-
-
0031949306
-
Duplication-based measures of difference between gene and species trees
-
Eulenstein O., Mirkin B., and Vingron M. Duplication-based measures of difference between gene and species trees. J. Comput. Biol. 5 (1998) 135-148
-
(1998)
J. Comput. Biol.
, vol.5
, pp. 135-148
-
-
Eulenstein, O.1
Mirkin, B.2
Vingron, M.3
-
30
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17 (1981) 368-376
-
(1981)
J. Mol. Evol.
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
31
-
-
0024152983
-
Phylogenies from molecular sequences: Inference and reliability
-
Felsenstein J. Phylogenies from molecular sequences: Inference and reliability. Annu. Rev. Genet. 22 (1988) 521-565
-
(1988)
Annu. Rev. Genet.
, vol.22
, pp. 521-565
-
-
Felsenstein, J.1
-
32
-
-
0003991673
-
-
Sinauer Associates, Sunderland, Massachusetts
-
Felsenstein J. Inferring Phylogenies (2004), Sinauer Associates, Sunderland, Massachusetts
-
(2004)
Inferring Phylogenies
-
-
Felsenstein, J.1
-
33
-
-
33244495782
-
Accuracy of coalescent likelihood estimates: Do we need more sites, more sequences, or more loci?
-
Felsenstein J. Accuracy of coalescent likelihood estimates: Do we need more sites, more sequences, or more loci?. Mol. Biol. Evol. 23 (2006) 691-700
-
(2006)
Mol. Biol. Evol.
, vol.23
, pp. 691-700
-
-
Felsenstein, J.1
-
34
-
-
0001735517
-
On the mathematical foundations of theoretical statistics
-
Fisher R.A. On the mathematical foundations of theoretical statistics. Phil. Trans. R. Soc. Lond. A 222 (1922) 309-368
-
(1922)
Phil. Trans. R. Soc. Lond. A
, vol.222
, pp. 309-368
-
-
Fisher, R.A.1
-
35
-
-
14844313275
-
Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree
-
Gadagkar S.R., Rosenberg M.S., and Kumar S. Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree. J. Exp. Zool. B 304B (2005) 64-74
-
(2005)
J. Exp. Zool. B
, vol.304 B
, pp. 64-74
-
-
Gadagkar, S.R.1
Rosenberg, M.S.2
Kumar, S.3
-
36
-
-
33644644463
-
Identification of ancestral genes introducing incongruence between gene and species trees
-
Gorbunov K.Y., and Lyubetsky V.A. Identification of ancestral genes introducing incongruence between gene and species trees. Mol. Biol. 39 (2005) 847-858
-
(2005)
Mol. Biol.
, vol.39
, pp. 847-858
-
-
Gorbunov, K.Y.1
Lyubetsky, V.A.2
-
38
-
-
0022376704
-
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
-
Hasegawa M., Kishino H., and Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22 (1985) 160-174
-
(1985)
J. Mol. Evol.
, vol.22
, pp. 160-174
-
-
Hasegawa, M.1
Kishino, H.2
Yano, T.3
-
39
-
-
77956890234
-
Monte carlo sampling methods using markov chain and their applications
-
Hastings W. Monte carlo sampling methods using markov chain and their applications. Biometrika 57 (1970) 97-109
-
(1970)
Biometrika
, vol.57
, pp. 97-109
-
-
Hastings, W.1
-
40
-
-
0027722963
-
Analysis of DNA sequence data: phylogenetic inference
-
Hillis D.M., Allard M.W., and Miyamoto M.M. Analysis of DNA sequence data: phylogenetic inference. Method Enzymol. 224 (1993) 456-487
-
(1993)
Method Enzymol.
, vol.224
, pp. 456-487
-
-
Hillis, D.M.1
Allard, M.W.2
Miyamoto, M.M.3
-
41
-
-
49249091441
-
Using supernetworks to distinguish hybridization from lineage-sorting
-
Holland B.R., Benthin S., Lockhart P.J., Moulton V., and Huber K.T. Using supernetworks to distinguish hybridization from lineage-sorting. BMC Evol. Biol. 8 (2008) 202
-
(2008)
BMC Evol. Biol.
, vol.8
, pp. 202
-
-
Holland, B.R.1
Benthin, S.2
Lockhart, P.J.3
Moulton, V.4
Huber, K.T.5
-
42
-
-
0026747106
-
Gene trees, species trees and the segregation of ancestral alleles
-
Hudson R.R. Gene trees, species trees and the segregation of ancestral alleles. Genetics 131 (1992) 509-512
-
(1992)
Genetics
, vol.131
, pp. 509-512
-
-
Hudson, R.R.1
-
44
-
-
26444512722
-
Reconstruction of reticulate networks from gene trees
-
Huson, D.H., Klopper, T., Lockhart, P.J., Steel, M.A., 2005. Reconstruction of reticulate networks from gene trees. In: Research in Computational Molecular Biology, Proceedings. pp. 233-249
-
(2005)
Research in Computational Molecular Biology, Proceedings
, pp. 233-249
-
-
Huson, D.H.1
Klopper, T.2
Lockhart, P.J.3
Steel, M.A.4
-
45
-
-
33846654919
-
-
Jin, G., Nakhleh, L., Snir, S., Tuller, T., 2006. Efficient parsimony-based methods for phylogenetic network reconstruction. Bioinformatics 23, e123-e128. Proceedings of the European Conference on Computational Biology.
-
Jin, G., Nakhleh, L., Snir, S., Tuller, T., 2006. Efficient parsimony-based methods for phylogenetic network reconstruction. Bioinformatics 23, e123-e128. Proceedings of the European Conference on Computational Biology.
-
-
-
-
46
-
-
33845886105
-
Inferring phylogenetic networks by the maximum parsimony criterion: a case study
-
Jin G., Nakhleh L., Snir S., and Tuller T. Inferring phylogenetic networks by the maximum parsimony criterion: a case study. Mol. Biol. Evol. 24 (2007) 324-337
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 324-337
-
-
Jin, G.1
Nakhleh, L.2
Snir, S.3
Tuller, T.4
-
48
-
-
33845412091
-
On the genealogy of large populations
-
Kingman J.F.C. On the genealogy of large populations. Stoch. Proc. Appl. 13 (1982) 235-248
-
(1982)
Stoch. Proc. Appl.
, vol.13
, pp. 235-248
-
-
Kingman, J.F.C.1
-
49
-
-
0034530345
-
Origins of the coalescent: 1974-1982
-
Kingman J.F.C. Origins of the coalescent: 1974-1982. Genetics 156 (2000) 1461-1463
-
(2000)
Genetics
, vol.156
, pp. 1461-1463
-
-
Kingman, J.F.C.1
-
50
-
-
33847302458
-
Inconsistency of phylogenetic estimates from concatenated data under coalescence
-
Kubatko L.S., and Degnan J.H. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 56 (2007) 17-24
-
(2007)
Syst. Biol.
, vol.56
, pp. 17-24
-
-
Kubatko, L.S.1
Degnan, J.H.2
-
51
-
-
63549118031
-
STEM: Species tree estimation using maximum likelihood for gene trees under coalescence
-
Kubatko L., Carstens B.C., and Knowles L.L. STEM: Species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 25 (2009) 971-973
-
(2009)
Bioinformatics
, vol.25
, pp. 971-973
-
-
Kubatko, L.1
Carstens, B.C.2
Knowles, L.L.3
-
52
-
-
0028177080
-
A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
-
Kuhner M.K., and Felsenstein J. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11 (1994) 459-468
-
(1994)
Mol. Biol. Evol.
, vol.11
, pp. 459-468
-
-
Kuhner, M.K.1
Felsenstein, J.2
-
53
-
-
34548081542
-
A likelihood framework to measure horizontal gene transfer
-
Linz S., Radtke A., and von Haeseler A. A likelihood framework to measure horizontal gene transfer. Mol. Biol. Evol. 24 (2007) 1312-1319
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 1312-1319
-
-
Linz, S.1
Radtke, A.2
von Haeseler, A.3
-
54
-
-
54949090066
-
BEST: Bayesian estimation of species trees under the coalescent model
-
Liu L. BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 24 (2008) 2542-2543
-
(2008)
Bioinformatics
, vol.24
, pp. 2542-2543
-
-
Liu, L.1
-
55
-
-
34548575126
-
Species trees from gene trees: Reconstructing bayesian posterior distributions of a species phylogeny using estimated gene tree distributions
-
Liu L., and Pearl D.K. Species trees from gene trees: Reconstructing bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 56 (2007) 504-514
-
(2007)
Syst. Biol.
, vol.56
, pp. 504-514
-
-
Liu, L.1
Pearl, D.K.2
-
56
-
-
47749093183
-
Estimating species trees using multiple-allele DNA sequence data
-
Liu L., Pearl D.K., Brumfield R.T., and Edwards S.V. Estimating species trees using multiple-allele DNA sequence data. Evolution 62 (2008) 2080-2091
-
(2008)
Evolution
, vol.62
, pp. 2080-2091
-
-
Liu, L.1
Pearl, D.K.2
Brumfield, R.T.3
Edwards, S.V.4
-
57
-
-
70350247510
-
-
Liu, L., Yu, L., Pearl, D.K., 2009a. Maximum tree: A consistent estimator of the species tree. J. Math. Biol. 10.1007/s00285-009-0260-0.
-
Liu, L., Yu, L., Pearl, D.K., 2009a. Maximum tree: A consistent estimator of the species tree. J. Math. Biol. 10.1007/s00285-009-0260-0.
-
-
-
-
58
-
-
70349425459
-
-
Liu, L., Yu, L., Pearl, D.K., Edwards, S.V., 2009b. Estimating species phylogenies using coalescence times among sequences. Syst. Biol., doi:10.1093/sysbio/syp031.
-
Liu, L., Yu, L., Pearl, D.K., Edwards, S.V., 2009b. Estimating species phylogenies using coalescence times among sequences. Syst. Biol., doi:10.1093/sysbio/syp031.
-
-
-
-
59
-
-
0034938644
-
From gene trees to species trees
-
Ma B., Li M., and Zhang L.X. From gene trees to species trees. SIAM J. Comput. 30 (2000) 729-752
-
(2000)
SIAM J. Comput.
, vol.30
, pp. 729-752
-
-
Ma, B.1
Li, M.2
Zhang, L.X.3
-
60
-
-
0031504952
-
Gene trees in species trees
-
Maddison W.P. Gene trees in species trees. Syst. Biol. 46 (1997) 523-536
-
(1997)
Syst. Biol.
, vol.46
, pp. 523-536
-
-
Maddison, W.P.1
-
61
-
-
33644606488
-
Inferring phylogeny despite incomplete lineage sorting
-
Maddison W.P., and Knowles L.L. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55 (2006) 21-30
-
(2006)
Syst. Biol.
, vol.55
, pp. 21-30
-
-
Maddison, W.P.1
Knowles, L.L.2
-
63
-
-
45849107980
-
The reticulate history of medicago (fabaceae)
-
Maureira-Butler I.J., Pfeil B.E., Muangprom A., Osborn T.C., and Doyle J.J. The reticulate history of medicago (fabaceae). Syst. Biol. 57 (2008) 466-482
-
(2008)
Syst. Biol.
, vol.57
, pp. 466-482
-
-
Maureira-Butler, I.J.1
Pfeil, B.E.2
Muangprom, A.3
Osborn, T.C.4
Doyle, J.J.5
-
64
-
-
58249136809
-
Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence. A model
-
Meng C., and Kubatko L.S. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence. A model. Theor. Popul. Biol. 75 (2009) 35-45
-
(2009)
Theor. Popul. Biol.
, vol.75
, pp. 35-45
-
-
Meng, C.1
Kubatko, L.S.2
-
66
-
-
33745512836
-
Reconstructing phylogenetic networks using maximum parsimony
-
Nakhleh, L., Jin, G., Zhao, F., Mellor-Crummey, J., 2005a. Reconstructing phylogenetic networks using maximum parsimony. In: Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference. pp. 93-102.
-
(2005)
Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
, pp. 93-102
-
-
Nakhleh, L.1
Jin, G.2
Zhao, F.3
Mellor-Crummey, J.4
-
67
-
-
26844458739
-
A fast and accurate heuristic for reconstructing horizontal gene transfer
-
Wang L. (Ed), Springer, Heidelberg
-
Nakhleh L., Ruths D., and Wang L.S. A fast and accurate heuristic for reconstructing horizontal gene transfer. In: Wang L. (Ed). Cocoon 2005. Lncs (2005), Springer, Heidelberg 84-93
-
(2005)
Cocoon 2005. Lncs
, pp. 84-93
-
-
Nakhleh, L.1
Ruths, D.2
Wang, L.S.3
-
68
-
-
0035400648
-
Gene trees and species trees are not the same
-
Nichols R. Gene trees and species trees are not the same. Trends Ecol. Evol. 16 (2001) 358-364
-
(2001)
Trends Ecol. Evol.
, vol.16
, pp. 358-364
-
-
Nichols, R.1
-
69
-
-
39749188544
-
Rooting the eutherian tree: the power and pitfalls of phylogenomics
-
Nishihara H., Okada N., and Hasegawa M. Rooting the eutherian tree: the power and pitfalls of phylogenomics. Genome Biol. 8 (2007) R199
-
(2007)
Genome Biol.
, vol.8
-
-
Nishihara, H.1
Okada, N.2
Hasegawa, M.3
-
70
-
-
0031774059
-
Genetree: comparing gene and species phylogenies using reconciled trees
-
Page R.D.M. Genetree: comparing gene and species phylogenies using reconciled trees. Bioinformatics 14 (1998) 819-820
-
(1998)
Bioinformatics
, vol.14
, pp. 819-820
-
-
Page, R.D.M.1
-
71
-
-
0033936591
-
Extracting species trees from complex gene trees: Reconciled trees and vertebrate phylogeny
-
Page R.D.M. Extracting species trees from complex gene trees: Reconciled trees and vertebrate phylogeny. Mol. Phylogenet. Evol. 14 (2000) 89-106
-
(2000)
Mol. Phylogenet. Evol.
, vol.14
, pp. 89-106
-
-
Page, R.D.M.1
-
72
-
-
0031110886
-
From gene to organismal phylogeny: reconciled trees and the gene tree species tree problem
-
Page R.D.M., and Charleston M.A. From gene to organismal phylogeny: reconciled trees and the gene tree species tree problem. Mol. Phylogenet. Evol. 7 (1997) 231-240
-
(1997)
Mol. Phylogenet. Evol.
, vol.7
, pp. 231-240
-
-
Page, R.D.M.1
Charleston, M.A.2
-
73
-
-
0023822631
-
Relationships between gene trees and species trees
-
Pamilo P., and Nei M. Relationships between gene trees and species trees. Mol. Biol. Evol. 5 (1988) 568-583
-
(1988)
Mol. Biol. Evol.
, vol.5
, pp. 568-583
-
-
Pamilo, P.1
Nei, M.2
-
74
-
-
33750437728
-
Widespread discordance of gene trees with species tree in drosophila: evidence for incomplete lineage sorting
-
Pollard D.A., Iyer V.N., Moses A.M., and Eisen M.B. Widespread discordance of gene trees with species tree in drosophila: evidence for incomplete lineage sorting. Plos Genet. 2 (2006) 1634-1647
-
(2006)
Plos Genet.
, vol.2
, pp. 1634-1647
-
-
Pollard, D.A.1
Iyer, V.N.2
Moses, A.M.3
Eisen, M.B.4
-
75
-
-
0025949736
-
Monophyly/paraphyly/polyphyly and gene/species trees - an example from drosophila
-
Powell J.R. Monophyly/paraphyly/polyphyly and gene/species trees - an example from drosophila. Mol. Biol. Evol. 8 (1991) 892-896
-
(1991)
Mol. Biol. Evol.
, vol.8
, pp. 892-896
-
-
Powell, J.R.1
-
76
-
-
52949152371
-
Phylogenetic inference using whole genomes
-
Rannala B., and Yang Z. Phylogenetic inference using whole genomes. Annu. Rev. Genom. Hum. Genet. 9 (2008) 217-231
-
(2008)
Annu. Rev. Genom. Hum. Genet.
, vol.9
, pp. 217-231
-
-
Rannala, B.1
Yang, Z.2
-
77
-
-
0041817551
-
Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci
-
Rannala B., and Yang Z.H. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164 (2003) 1645-1656
-
(2003)
Genetics
, vol.164
, pp. 1645-1656
-
-
Rannala, B.1
Yang, Z.H.2
-
78
-
-
0036515730
-
The probability of topological concordance of gene trees and species trees
-
Rosenberg N.A. The probability of topological concordance of gene trees and species trees. Theor. Popul. Biol. 61 (2002) 225-247
-
(2002)
Theor. Popul. Biol.
, vol.61
, pp. 225-247
-
-
Rosenberg, N.A.1
-
79
-
-
0023375195
-
The neighbor-joining method - a new method for reconstructing phylogenetic trees
-
Saitou N., and Nei M. The neighbor-joining method - a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 (1987) 406-425
-
(1987)
Mol. Biol. Evol.
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
80
-
-
34248217100
-
Inferring angiosperm phylogeny from est data with widespread gene duplication
-
Sanderson M.J., and McMahon M.M. Inferring angiosperm phylogeny from est data with widespread gene duplication. BMC Evol. Biol. 7 Suppl 1 (2007) S3
-
(2007)
BMC Evol. Biol.
, vol.7
, Issue.SUPPL. 1
-
-
Sanderson, M.J.1
McMahon, M.M.2
-
81
-
-
15444373349
-
Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data
-
Seo T.K., Kishino H., and Thorne J.L. Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data. Proc. Natl. Acad. Sci. USA 102 (2005) 4436-4441
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 4436-4441
-
-
Seo, T.K.1
Kishino, H.2
Thorne, J.L.3
-
82
-
-
0031296691
-
Inferring species trees from gene trees: a phylogenetic analysis of the elapidae (serpentes) based on the amino acid sequences of venom proteins
-
Slowinski J.B., Knight A., and Rooney A.P. Inferring species trees from gene trees: a phylogenetic analysis of the elapidae (serpentes) based on the amino acid sequences of venom proteins. Mol. Phylogenet. Evol. 8 (1997) 349-362
-
(1997)
Mol. Phylogenet. Evol.
, vol.8
, pp. 349-362
-
-
Slowinski, J.B.1
Knight, A.2
Rooney, A.P.3
-
83
-
-
41849131023
-
Maximum likelihood supertrees
-
Steel M., and Rodrigo A. Maximum likelihood supertrees. Syst. Biol. 57 (2008) 243-250
-
(2008)
Syst. Biol.
, vol.57
, pp. 243-250
-
-
Steel, M.1
Rodrigo, A.2
-
84
-
-
84948965737
-
Gene trees and species trees: The gene-duplication problem is fixed-parameter tractable
-
Stege, U., 1999. Gene trees and species trees: The gene-duplication problem is fixed-parameter tractable. Algorithms and data structures. pp. 288-293
-
(1999)
Algorithms and data structures
, pp. 288-293
-
-
Stege, U.1
-
85
-
-
19944407429
-
Maximum-likelihood methods for phylogeny estimation
-
Sullivan J. Maximum-likelihood methods for phylogeny estimation. Methods Enzymol. 395 (2005) 757-779
-
(2005)
Methods Enzymol.
, vol.395
, pp. 757-779
-
-
Sullivan, J.1
-
86
-
-
0001336205
-
Phylogenetic Inference
-
D.M. Hillis, C. Moritz, B.K. Mable, Eds, Sinauer, Sunderland, MA
-
Swofford, D.L., Olsen, G.J., Waddell, P.J., Hillis, D.M., 1996. Phylogenetic Inference. In: D.M. Hillis, C. Moritz, B.K. Mable, (Eds.), Molecular Systematics. Sinauer, Sunderland, MA.
-
(1996)
Molecular Systematics
-
-
Swofford, D.L.1
Olsen, G.J.2
Waddell, P.J.3
Hillis, D.M.4
-
87
-
-
0024713112
-
Gene genealogy in three related populations: Consistency probability between gene and population trees
-
Takahata N. Gene genealogy in three related populations: Consistency probability between gene and population trees. Genetics 122 (1989) 957-966
-
(1989)
Genetics
, vol.122
, pp. 957-966
-
-
Takahata, N.1
-
88
-
-
70350547715
-
Integrating sequence and topology for efficient and accurate detection of horizontal gene transfer
-
Proceedings of the Sixth RECOMB Comparative Genomics Satellite Workshop
-
Than, C., Jin, G., Nakhleh, L., 2008. Integrating sequence and topology for efficient and accurate detection of horizontal gene transfer. In: Proceedings of the Sixth RECOMB Comparative Genomics Satellite Workshop. Lecture Notes in Bioinformatics. pp. 113-127.
-
(2008)
Lecture Notes in Bioinformatics. pp
, vol.113-127
-
-
Than, C.1
Jin, G.2
Nakhleh, L.3
-
89
-
-
0036407127
-
Tree reconciliation: reconstruction of species phylogeny by phylogenetic gene trees
-
V'Yugin V.V., Gelfand M.S., and Lyubetsky V.A. Tree reconciliation: reconstruction of species phylogeny by phylogenetic gene trees. Mol. Biol. 36 (2002) 650-658
-
(2002)
Mol. Biol.
, vol.36
, pp. 650-658
-
-
V'Yugin, V.V.1
Gelfand, M.S.2
Lyubetsky, V.A.3
-
91
-
-
0035031966
-
A general empirical model of protein evolution derived from multiple protein families using a maximum likelihood approach
-
Whelan S., and Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum likelihood approach. Mol. Biol. Evol. 18 (2001) 691-699
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 691-699
-
-
Whelan, S.1
Goldman, N.2
-
92
-
-
22844442070
-
The shape of supertrees to come: tree shape related properties of 14 supertree methods
-
Wilkinson M., Cotton J.A., Creevey C., Eulenstein O., Harris S.R., Lapointe F.J., Levasseur C., McInerney J.O., Pisani D., and Thorley J.L. The shape of supertrees to come: tree shape related properties of 14 supertree methods. Syst. Biol. 54 (2005) 419-431
-
(2005)
Syst. Biol.
, vol.54
, pp. 419-431
-
-
Wilkinson, M.1
Cotton, J.A.2
Creevey, C.3
Eulenstein, O.4
Harris, S.R.5
Lapointe, F.J.6
Levasseur, C.7
McInerney, J.O.8
Pisani, D.9
Thorley, J.L.10
|