-
1
-
-
0031504952
-
Gene Trees in Species Trees
-
Maddison WP. Gene Trees in Species Trees. Systematic Biology 1997, 46:523-536.
-
(1997)
Systematic Biology
, vol.46
, pp. 523-536
-
-
Maddison, W.P.1
-
2
-
-
33646928341
-
Discordance of Species Trees with Their Most Likely Gene Trees
-
10.1371/journal.pgen.0020068, 1464820, 16733550
-
Degnan JH, Rosenberg NA. Discordance of Species Trees with Their Most Likely Gene Trees. PLoS Genetics 2006, 2(5):e68. 10.1371/journal.pgen.0020068, 1464820, 16733550.
-
(2006)
PLoS Genetics
, vol.2
, Issue.5
-
-
Degnan, J.H.1
Rosenberg, N.A.2
-
3
-
-
0000365320
-
Fitting the gene lineage into its species lineage. A parsimony strategy illustrated by cladograms constructed from globin sequences
-
Goodman M, Czelusniak J, Moore GW, Romero-Herrera AE, Matsuda G. Fitting the gene lineage into its species lineage. A parsimony strategy illustrated by cladograms constructed from globin sequences. Systematic Zoology 1979, 28:132-163.
-
(1979)
Systematic Zoology
, vol.28
, pp. 132-163
-
-
Goodman, M.1
Czelusniak, J.2
Moore, G.W.3
Romero-Herrera, A.E.4
Matsuda, G.5
-
4
-
-
12044253257
-
Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas
-
Page RDM. Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Systematic Biology 1994, 43:58-77.
-
(1994)
Systematic Biology
, vol.43
, pp. 58-77
-
-
Page, R.D.M.1
-
5
-
-
0030253222
-
Reconstruction of Ancient Molecular Phylogeny
-
10.1006/mpev.1996.0071, 8899723
-
Guigó R, Muchnik I, Smith TF. Reconstruction of Ancient Molecular Phylogeny. Molecular Phylogenetics and Evolution 1996, 6(2):189-213. 10.1006/mpev.1996.0071, 8899723.
-
(1996)
Molecular Phylogenetics and Evolution
, vol.6
, Issue.2
, pp. 189-213
-
-
Guigó, R.1
Muchnik, I.2
Smith, T.F.3
-
6
-
-
0029448349
-
A Biologically Consistent Model for Comparing Molecular Phylogenies
-
10.1089/cmb.1995.2.493, 8634901
-
Mirkin B, Muchnik I, Smith TF. A Biologically Consistent Model for Comparing Molecular Phylogenies. Journal of Computational Biology 1995, 2(4):493-507. 10.1089/cmb.1995.2.493, 8634901.
-
(1995)
Journal of Computational Biology
, vol.2
, Issue.4
, pp. 493-507
-
-
Mirkin, B.1
Muchnik, I.2
Smith, T.F.3
-
8
-
-
0033723163
-
New algorithms for the duplication-loss model
-
Hallett MT, Lagergren J. New algorithms for the duplication-loss model. RECOMB 2000, 138-146.
-
(2000)
RECOMB
, pp. 138-146
-
-
Hallett, M.T.1
Lagergren, J.2
-
9
-
-
27844468683
-
Reconciling a gene tree to a species tree under the duplication cost model
-
Bonizzoni P, Vedova GD, Dondi R. Reconciling a gene tree to a species tree under the duplication cost model. Theor Comput Sci 2005, 347(1-2):36-53.
-
(2005)
Theor Comput Sci
, vol.347
, Issue.1-2
, pp. 36-53
-
-
Bonizzoni, P.1
Vedova, G.D.2
Dondi, R.3
-
10
-
-
33746345337
-
DLS-trees: A model of evolutionary scenarios
-
Górecki P, Tiuryn J. DLS-trees: A model of evolutionary scenarios. Theor Comput Sci 2006, 359(1-3):378-399.
-
(2006)
Theor Comput Sci
, vol.359
, Issue.1-3
, pp. 378-399
-
-
Górecki, P.1
Tiuryn, J.2
-
11
-
-
33645981936
-
A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction
-
10.1089/cmb.2006.13.320, 16597243
-
Durand D, Halldórsson BV, Vernot B. A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction. Journal of Computational Biology 2006, 13(2):320-335. 10.1089/cmb.2006.13.320, 16597243.
-
(2006)
Journal of Computational Biology
, vol.13
, Issue.2
, pp. 320-335
-
-
Durand, D.1
Halldórsson, B.V.2
Vernot, B.3
-
12
-
-
52449122374
-
Gene Family Evolution by Duplication, Speciation, and Loss
-
10.1089/cmb.2008.0054, 18781833
-
Chauve C, Doyon JP, El-Mabrouk N. Gene Family Evolution by Duplication, Speciation, and Loss. Journal of Computational Biology 2008, 15(8):1043-1062. 10.1089/cmb.2008.0054, 18781833.
-
(2008)
Journal of Computational Biology
, vol.15
, Issue.8
, pp. 1043-1062
-
-
Chauve, C.1
Doyon, J.P.2
El-Mabrouk, N.3
-
13
-
-
67650324396
-
New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees
-
Chauve C, El-Mabrouk N. New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees. RECOMB 2009, 46-58.
-
(2009)
RECOMB
, pp. 46-58
-
-
Chauve, C.1
El-Mabrouk, N.2
-
14
-
-
33644606488
-
Inferring Phylogeny Despite Incomplete Lineage Sorting
-
10.1080/10635150500354928, 16507521
-
Maddison WP, Knowles LL. Inferring Phylogeny Despite Incomplete Lineage Sorting. Systematic Biology 2006, 55:21-30. 10.1080/10635150500354928, 16507521.
-
(2006)
Systematic Biology
, vol.55
, pp. 21-30
-
-
Maddison, W.P.1
Knowles, L.L.2
-
15
-
-
75149146844
-
Inferring a Species Tree from Gene Trees under the Deep Coalescence Cost
-
Zhang L. Inferring a Species Tree from Gene Trees under the Deep Coalescence Cost. RECOMB 2000, 192-193.
-
(2000)
RECOMB
, pp. 192-193
-
-
Zhang, L.1
-
16
-
-
70349658769
-
Species tree inference by minimizing deep coalescences
-
10.1371/journal.pcbi.1000501, 2729383, 19749978
-
Than C, Nakhleh L. Species tree inference by minimizing deep coalescences. PLoS Computational Biology 2009, 5(9):e1000501. 10.1371/journal.pcbi.1000501, 2729383, 19749978.
-
(2009)
PLoS Computational Biology
, vol.5
, Issue.9
-
-
Than, C.1
Nakhleh, L.2
-
17
-
-
0034938644
-
From Gene Trees to Species Trees
-
Ma B, Li M, Zhang L. From Gene Trees to Species Trees. SIAM J Comput 2000, 30(3):729-752.
-
(2000)
SIAM J Comput
, vol.30
, Issue.3
, pp. 729-752
-
-
Ma, B.1
Li, M.2
Zhang, L.3
-
18
-
-
13844266486
-
On the computational complexity of the rooted subtree prune and regraft distance
-
Bordewich M, Semple C. On the computational complexity of the rooted subtree prune and regraft distance. Annals of Combinatorics 2004, 8:409-423.
-
(2004)
Annals of Combinatorics
, vol.8
, pp. 409-423
-
-
Bordewich, M.1
Semple, C.2
-
19
-
-
55249097586
-
Improved Heuristics for Minimum-Flip Supertree Construction
-
Chen D, Eulenstein O, Fernández-Baca D, Burleigh JG. Improved Heuristics for Minimum-Flip Supertree Construction. Evolutionary Bioinformatics 2006, 2:347-356.
-
(2006)
Evolutionary Bioinformatics
, vol.2
, pp. 347-356
-
-
Chen, D.1
Eulenstein, O.2
Fernández-Baca, D.3
Burleigh, J.G.4
-
20
-
-
0031774059
-
Comparing gene and species phylogenies using reconciled trees
-
10.1093/bioinformatics/14.9.819, 9918954
-
Page RDM. comparing gene and species phylogenies using reconciled trees. Bioinformatics 1998, 14(9):819-820. 10.1093/bioinformatics/14.9.819, 9918954.
-
(1998)
Bioinformatics
, vol.14
, Issue.9
, pp. 819-820
-
-
Page, R.D.M.1
-
21
-
-
3042649996
-
Mesquite: a modular system for evolutionary analysis. Version 2.6
-
Maddison WP, Maddison D. Mesquite: a modular system for evolutionary analysis. Version 2.6. 2009, , http://mesquiteproject.org
-
(2009)
-
-
Maddison, W.P.1
Maddison, D.2
-
22
-
-
34547428923
-
Heuristics for the Gene-Duplication Problem: A Θ(n) Speed-Up for the Local Search
-
Bansal MS, Burleigh JG, Eulenstein O, Wehe A. Heuristics for the Gene-Duplication Problem: A Θ(n) Speed-Up for the Local Search. RECOMB 2007, 238-252.
-
(2007)
RECOMB
, pp. 238-252
-
-
Bansal, M.S.1
Burleigh, J.G.2
Eulenstein, O.3
Wehe, A.4
-
24
-
-
34548575126
-
Species Trees from Gene Trees: Reconstructing Bayesian Posterior Distributions of a Species Phylogeny Using Estimated Gene Tree Distributions
-
10.1080/10635150701429982, 17562474
-
Liu L, Pearl DK. Species Trees from Gene Trees: Reconstructing Bayesian Posterior Distributions of a Species Phylogeny Using Estimated Gene Tree Distributions. Systematic Biology 2007, 56(3):504-514. 10.1080/10635150701429982, 17562474.
-
(2007)
Systematic Biology
, vol.56
, Issue.3
, pp. 504-514
-
-
Liu, L.1
Pearl, D.K.2
-
25
-
-
63549118031
-
STEM: species tree estimation using maximum likelihood for gene trees under coalescence
-
10.1093/bioinformatics/btp079, 19211573
-
Kubatko LS, Carstens BC, Knowles LL. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 2009, 25(7):971-973. 10.1093/bioinformatics/btp079, 19211573.
-
(2009)
Bioinformatics
, vol.25
, Issue.7
, pp. 971-973
-
-
Kubatko, L.S.1
Carstens, B.C.2
Knowles, L.L.3
-
26
-
-
34547677806
-
Bayesian Estimation of Concordance Among Gene Trees
-
Ané C, Larget B, Baum DA, Smith SD, Rokas A. Bayesian Estimation of Concordance Among Gene Trees. Mol Biol Evol 2007, 24(7):1575.
-
(2007)
Mol Biol Evol
, vol.24
, Issue.7
, pp. 1575
-
-
Ané, C.1
Larget, B.2
Baum, D.A.3
Smith, S.D.4
Rokas, A.5
-
28
-
-
65249107239
-
Simultaneous Bayesian gene tree reconstruction and reconciliation analysis
-
Äkerborg O, Sennblad B, Arvestad L, Lagergren J. Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proceedings of the National Academy of Sciences 2009, 106(14):5714-5719.
-
(2009)
Proceedings of the National Academy of Sciences
, vol.106
, Issue.14
, pp. 5714-5719
-
-
Äkerborg, O.1
Sennblad, B.2
Arvestad, L.3
Lagergren, J.4
-
29
-
-
75149178305
-
Algorithms for efficient phylogenetic tree construction
-
Iowa State Univ
-
Bansal MS. Algorithms for efficient phylogenetic tree construction. PhD thesis 2009, Iowa State Univ.
-
(2009)
PhD thesis
-
-
Bansal, M.S.1
-
30
-
-
0242365676
-
Genome-scale approaches to resolving incongruence in molecular phylogenies
-
10.1038/nature02053, 14574403
-
Rokas A, Williams BL, King N, Carroll SB. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 2003, 425:798-804. 10.1038/nature02053, 14574403.
-
(2003)
Nature
, vol.425
, pp. 798-804
-
-
Rokas, A.1
Williams, B.L.2
King, N.3
Carroll, S.B.4
-
31
-
-
56449101000
-
The Apicomplexan Whole-Genome Phylogeny: An Analysis of Incongruence among Gene Trees
-
10.1093/molbev/msn213, 2582981, 18820254
-
Kuo CH, Wares JP, Kissinger JC. The Apicomplexan Whole-Genome Phylogeny: An Analysis of Incongruence among Gene Trees. Mol Biol Evol 2008, 25(12):2689-2698. 10.1093/molbev/msn213, 2582981, 18820254.
-
(2008)
Mol Biol Evol
, vol.25
, Issue.12
, pp. 2689-2698
-
-
Kuo, C.H.1
Wares, J.P.2
Kissinger, J.C.3
-
32
-
-
33750403801
-
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
10.1093/bioinformatics/btl446, 16928733
-
Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22(21):2688-2690. 10.1093/bioinformatics/btl446, 16928733.
-
(2006)
Bioinformatics
, vol.22
, Issue.21
, pp. 2688-2690
-
-
Stamatakis, A.1
-
33
-
-
84874648550
-
Genome-scale phylogenetics: inferring the plant tree of life from 18,896 discordant gene trees
-
Burleigh JG, Bansal MS, Eulenstein O, Hartmann S, Wehe A, Vision TJ. Genome-scale phylogenetics: inferring the plant tree of life from 18,896 discordant gene trees. Systematic Biology
-
Systematic Biology
-
-
Burleigh, J.G.1
Bansal, M.S.2
Eulenstein, O.3
Hartmann, S.4
Wehe, A.5
Vision, T.J.6
-
35
-
-
46249126320
-
DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony
-
10.1093/bioinformatics/btn230, 18474508
-
Wehe A, Bansal MS, Burleigh JG, Eulenstein O. DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics 2008, 24(13). 10.1093/bioinformatics/btn230, 18474508.
-
(2008)
Bioinformatics
, vol.24
, Issue.13
-
-
Wehe, A.1
Bansal, M.S.2
Burleigh, J.G.3
Eulenstein, O.4
-
36
-
-
19944410649
-
Tangled tales from multiple markers: reconciling conflict between phylogenies to build molecular supertrees
-
Springer-Verlag, Bininda-Emonds ORP
-
Cotton JA, Page RDM. Tangled tales from multiple markers: reconciling conflict between phylogenies to build molecular supertrees. Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life 2004, 107-125. Springer-Verlag, Bininda-Emonds ORP.
-
(2004)
Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life
, pp. 107-125
-
-
Cotton, J.A.1
Page, R.D.M.2
|