-
1
-
-
0031504952
-
Gene trees in species trees
-
Maddison WP. Gene trees in species trees. Syst. Biol 1997, 46:523-536.
-
(1997)
Syst. Biol
, vol.46
, pp. 523-536
-
-
Maddison, W.P.1
-
2
-
-
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. Syst. Zool 1979, 28:132-163.
-
(1979)
Syst. Zool
, vol.28
, pp. 132-163
-
-
Goodman, M.1
Czelusniak, J.2
Moore, G.W.3
Romero-Herrera, A.E.4
Matsuda, G.5
-
4
-
-
0031296691
-
Inferring Species Trees from Gene Trees: A Phylogenetic Analysis of the Elapidae (Serpentes) Based on the Amino Acid Sequences of Venom Proteins
-
10.1006/mpev.1997.0434, 9417893
-
Slowinski JB, Knight A, Rooney AP. 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. 1997, 8(3):349-362. 10.1006/mpev.1997.0434, 9417893.
-
(1997)
Mol. Phylogenet. Evol.
, vol.8
, Issue.3
, pp. 349-362
-
-
Slowinski, J.B.1
Knight, A.2
Rooney, A.P.3
-
6
-
-
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, Volume 4453 of LNCS 2007, 238-252.
-
(2007)
RECOMB, Volume 4453 of LNCS
, pp. 238-252
-
-
Bansal, M.S.1
Burleigh, J.G.2
Eulenstein, O.3
Wehe, A.4
-
7
-
-
46249126320
-
Dup-Tree: a program for large-scale phylogenetic analyses using gene tree parsimony
-
10.1093/bioinformatics/btn230, 18474508
-
Wehe A, Bansal MS, Burleigh JG, Eulenstein O. Dup-Tree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics 2008, 24(13):1540-1541. 10.1093/bioinformatics/btn230, 18474508.
-
(2008)
Bioinformatics
, vol.24
, Issue.13
, pp. 1540-1541
-
-
Wehe, A.1
Bansal, M.S.2
Burleigh, J.G.3
Eulenstein, O.4
-
8
-
-
0033936591
-
Extracting Species Trees From Complex Gene Trees: Reconciled Trees And Vertebrate Phylogeny
-
10.1006/mpev.1999.0676, 10631044
-
Page RDM. Extracting Species Trees From Complex Gene Trees: Reconciled Trees And Vertebrate Phylogeny. Mol. Phylogenet. Evol. 2000, 14:89-106. 10.1006/mpev.1999.0676, 10631044.
-
(2000)
Mol. Phylogenet. Evol.
, vol.14
, pp. 89-106
-
-
Page, R.D.M.1
-
9
-
-
0037036630
-
Going Nuclear: Gene Family Evolution And Vertebrate Phylogeny Reconciled
-
10.1098/rspb.2002.2074, 1691073, 12184825
-
Cotton JA, Page RDM. Going Nuclear: Gene Family Evolution And Vertebrate Phylogeny Reconciled. Proc Biol Sci 2002, 269:1555-1561. 10.1098/rspb.2002.2074, 1691073, 12184825.
-
(2002)
Proc Biol Sci
, vol.269
, pp. 1555-1561
-
-
Cotton, J.A.1
Page, R.D.M.2
-
10
-
-
0036699004
-
Perils of Paralogy: Using HSP70 Genes for Inferring Organismal Phylogenies
-
10.1080/10635150290069995, 12228000
-
Martin AP, Burg TM. Perils of Paralogy: Using HSP70 Genes for Inferring Organismal Phylogenies. Syst. Biol. 2002, 51(4):570-587. 10.1080/10635150290069995, 12228000.
-
(2002)
Syst. Biol.
, vol.51
, Issue.4
, pp. 570-587
-
-
Martin, A.P.1
Burg, T.M.2
-
11
-
-
56549101000
-
The Vestigial Olfactory Receptor Subgenome of Odontocete Whales: Phylogenetic Congruence between Gene-Tree Reconciliation and Supermatrix Methods
-
10.1080/10635150802304787, 18686195
-
McGowen MR, Clark C, Gatesy J. The Vestigial Olfactory Receptor Subgenome of Odontocete Whales: Phylogenetic Congruence between Gene-Tree Reconciliation and Supermatrix Methods. Syst. Biol. 2008, 57(4):574-590. 10.1080/10635150802304787, 18686195.
-
(2008)
Syst. Biol.
, vol.57
, Issue.4
, pp. 574-590
-
-
McGowen, M.R.1
Clark, C.2
Gatesy, J.3
-
12
-
-
34447314849
-
The Traveling Salesman Problem: A Computational Study (Princeton Series in Applied Mathematics)
-
Princeton University Press
-
Applegate DL, Bixby RE, Chvatal V, Cook WJ. The Traveling Salesman Problem: A Computational Study (Princeton Series in Applied Mathematics). 2007, Princeton University Press.
-
(2007)
-
-
Applegate, D.L.1
Bixby, R.E.2
Chvatal, V.3
Cook, W.J.4
-
14
-
-
79951533855
-
Branch-and-Bound Approach for Parsimonious Inference of a Species Tree From a Set of Gene Family Trees
-
LIRMM
-
Doyon JP, Chauve C. Branch-and-Bound Approach for Parsimonious Inference of a Species Tree From a Set of Gene Family Trees. Tech. rep. 2010, LIRMM.
-
(2010)
Tech. rep.
-
-
Doyon, J.P.1
Chauve, C.2
-
16
-
-
34248217100
-
Inferring angiosperm phylogeny from EST data with widespread gene duplication
-
10.1186/1471-2148-7-S1-S3, 1796612, 17288576
-
Sanderson MJ, McMahon M. Inferring angiosperm phylogeny from EST data with widespread gene duplication. BMC Evol. Biol. 2007, 7(Suppl 1):S3. 10.1186/1471-2148-7-S1-S3, 1796612, 17288576.
-
(2007)
BMC Evol. Biol.
, vol.7
, Issue.SUPPL 1
-
-
Sanderson, M.J.1
McMahon, M.2
-
17
-
-
33646728443
-
Integer Programming Approaches to Haplotype Inference by Pure Parsimony
-
Brown DG, Harrower IM. Integer Programming Approaches to Haplotype Inference by Pure Parsimony. IEEE/ACM Trans. Comput. Biol. Bioinf. 2006, 3(2):141-154.
-
(2006)
IEEE/ACM Trans. Comput. Biol. Bioinf.
, vol.3
, Issue.2
, pp. 141-154
-
-
Brown, D.G.1
Harrower, I.M.2
-
18
-
-
77249117825
-
Constructing majority-rule supertrees
-
10.1186/1748-7188-5-2, 2826330, 20047658
-
Dong J, Fernández-Baca D, McMorris FR. Constructing majority-rule supertrees. Algorithms for Molecular Biology 2010, 5:2. 10.1186/1748-7188-5-2, 2826330, 20047658.
-
(2010)
Algorithms for Molecular Biology
, vol.5
, pp. 2
-
-
Dong, J.1
Fernández-Baca, D.2
McMorris, F.R.3
-
19
-
-
67650337321
-
The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory
-
Gusfield D. The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory. RECOMB 2009, 236-252.
-
(2009)
RECOMB
, pp. 236-252
-
-
Gusfield, D.1
-
20
-
-
37849054103
-
Integer Programming Formulations and Computations Solving Phylogenetic and Population Genetic Problems with Missing or Genotypic Data
-
Gusfield D, Frid Y, Brown DG. Integer Programming Formulations and Computations Solving Phylogenetic and Population Genetic Problems with Missing or Genotypic Data. COCOON 2007, 51-64.
-
(2007)
COCOON
, pp. 51-64
-
-
Gusfield, D.1
Frid, Y.2
Brown, D.G.3
-
21
-
-
34547439745
-
Efficiently finding the most parsimonious phylogenetic tree via linear programming
-
Sridhar S, Lam F, Blelloch GE, Ravi R, Schwartz R. Efficiently finding the most parsimonious phylogenetic tree via linear programming. Int. J. Bioinf. Res. Appl. 2007, 4463:37-48.
-
(2007)
Int. J. Bioinf. Res. Appl.
, vol.4463
, pp. 37-48
-
-
Sridhar, S.1
Lam, F.2
Blelloch, G.E.3
Ravi, R.4
Schwartz, R.5
-
22
-
-
77958063731
-
Exact ILP Solutions for Phylogenetic Minimum Flip Problems
-
Chimani M, Rahmann S, Sebastian B. Exact ILP Solutions for Phylogenetic Minimum Flip Problems. Proc. ACM BCB 2010, 147-153.
-
(2010)
Proc. ACM BCB
, pp. 147-153
-
-
Chimani, M.1
Rahmann, S.2
Sebastian, B.3
-
23
-
-
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 Comput. Biol. 2009, 5(9):e1000501. 10.1371/journal.pcbi.1000501, 2729383, 19749978.
-
(2009)
PLoS Comput. Biol.
, vol.5
, Issue.9
-
-
Than, C.1
Nakhleh, L.2
-
24
-
-
33749579169
-
Vorhersage von Genduplikationen und deren Entwicklung in der Evolution
-
University of Bonn
-
Eulenstein O. Vorhersage von Genduplikationen und deren Entwicklung in der Evolution. PhD dissertation 1998, University of Bonn.
-
(1998)
PhD dissertation
-
-
Eulenstein, O.1
-
25
-
-
0042601470
-
Phylogenetics
-
Oxford University Press
-
Semple C, Steel MA. Phylogenetics. 2003, Oxford University Press.
-
(2003)
-
-
Semple, C.1
Steel, M.A.2
-
26
-
-
0004137004
-
Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology
-
Cambridge University Press
-
Gusfield D. Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. 1997, Cambridge University Press.
-
(1997)
-
-
Gusfield, D.1
-
27
-
-
84987049379
-
Efficient algorithms for inferring evolutionary trees
-
Gusfield D. Efficient algorithms for inferring evolutionary trees. Networks 1991, 21:19-28.
-
(1991)
Networks
, vol.21
, pp. 19-28
-
-
Gusfield, D.1
-
28
-
-
84874758799
-
Gurobi Optimization 2.0.2
-
Gurobi Optimization, Inc
-
Gurobi Optimization, Inc Gurobi Optimization 2.0.2. 2010, Gurobi Optimization, Inc., http://www.gurobi.com/
-
(2010)
-
-
-
29
-
-
79951534528
-
IBM ILOG CPLEX 12.1
-
IBM, Inc
-
IBM, Inc IBM ILOG CPLEX 12.1. 2009, IBM, Inc., http://www.ibm.com/software/integration/optimization/cplex/
-
(2009)
-
-
-
30
-
-
33344478092
-
Phytome: a platform for plant comparative genomics
-
Database issue, 10.1093/nar/gkj045, 1347408, 16381967
-
Hartmann S, Lu D, Phillips J, Vision TJ. Phytome: a platform for plant comparative genomics. Nucleic Acids Res 2006, 34(Database issue):D724-D730. 10.1093/nar/gkj045, 1347408, 16381967.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Hartmann, S.1
Lu, D.2
Phillips, J.3
Vision, T.J.4
-
31
-
-
43249090276
-
Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment?
-
10.1186/1471-2148-8-95, 2359737, 18366758
-
Hartmann S, Vision TJ. Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment?. BMC Evol. Biol. 2008, 8:95. 10.1186/1471-2148-8-95, 2359737, 18366758.
-
(2008)
BMC Evol. Biol.
, vol.8
, pp. 95
-
-
Hartmann, S.1
Vision, T.J.2
-
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
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 1992, 8(3):275-282.
-
(1992)
Comput. Appl. Biosci.
, vol.8
, Issue.3
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
34
-
-
47949090280
-
PHYLIP (Phylogeny Inference Package) version 3.6
-
Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author 2005,
-
(2005)
Distributed by the author
-
-
Felsenstein, J.1
-
35
-
-
10644238478
-
Phylogenetic signal in nucleotide data from seed plants: Implications for resolving the seed plant tree of life
-
Burleigh JG, Mathews S. Phylogenetic signal in nucleotide data from seed plants: Implications for resolving the seed plant tree of life. Am. J. Bot. 2004, 91(10):1599-1613.
-
(2004)
Am. J. Bot.
, vol.91
, Issue.10
, pp. 1599-1613
-
-
Burleigh, J.G.1
Mathews, S.2
-
36
-
-
0034628615
-
Seed plant phylogeny: Demise of the anthophyte hypothesis?
-
10.1016/S0960-9822(00)00304-3, 10679315
-
Donoghue MJ, Doyle JA. Seed plant phylogeny: Demise of the anthophyte hypothesis?. Current Biology 2000, 10(3):R106-R109. 10.1016/S0960-9822(00)00304-3, 10679315.
-
(2000)
Current Biology
, vol.10
, Issue.3
-
-
Donoghue, M.J.1
Doyle, J.A.2
-
37
-
-
0036950836
-
Relationships among Seed Plants Inferred from Highly Conserved Genes: Sorting Conflicting Phylogenetic Signals among Ancient Lineages
-
Magallón S, Sanderson MJ. Relationships among Seed Plants Inferred from Highly Conserved Genes: Sorting Conflicting Phylogenetic Signals among Ancient Lineages. Am. J. Bot. 2002, 89(12):1991-2006.
-
(2002)
Am. J. Bot.
, vol.89
, Issue.12
, pp. 1991-2006
-
-
Magallón, S.1
Sanderson, M.J.2
-
38
-
-
60249093425
-
Phylogenetic relationships among seed plants: Persistent questions and the limits of molecular data
-
Mathews S. Phylogenetic relationships among seed plants: Persistent questions and the limits of molecular data. Am. J. Bot. 2009, 96:228-236.
-
(2009)
Am. J. Bot.
, vol.96
, pp. 228-236
-
-
Mathews, S.1
-
39
-
-
0036800892
-
Phylogeny of Seed Plants Based on Evidence from Eight Genes
-
Soltis DE, Soltis PS, Zanis MJ. Phylogeny of Seed Plants Based on Evidence from Eight Genes. Am. J. Bot. 2002, 89(10):1670-1681.
-
(2002)
Am. J. Bot.
, vol.89
, Issue.10
, pp. 1670-1681
-
-
Soltis, D.E.1
Soltis, P.S.2
Zanis, M.J.3
-
40
-
-
0000863074
-
Phylogenetic Analysis of Seed Plants and the Origin of Angiosperms
-
Crane PR. Phylogenetic Analysis of Seed Plants and the Origin of Angiosperms. Annals of the Missouri Botanical Garden 1985, 72:716-793.
-
(1985)
Annals of the Missouri Botanical Garden
, vol.72
, pp. 716-793
-
-
Crane, P.R.1
-
42
-
-
0001234321
-
Seed plant phylogeny and the origin of angiosperms: An experimental cladistic approach
-
Doyle JA, Donoghue MJ. Seed plant phylogeny and the origin of angiosperms: An experimental cladistic approach. The Botanical Review 1986, 52(4):321-431.
-
(1986)
The Botanical Review
, vol.52
, Issue.4
, pp. 321-431
-
-
Doyle, J.A.1
Donoghue, M.J.2
-
44
-
-
0000271756
-
A Reevaluation of Seed Plant Phylogeny
-
Nixon KC, Crepet WL, Stevenson DW, Friis EM. A Reevaluation of Seed Plant Phylogeny. Annals of the Missouri Botanical Garden 1994, 81(3):484-533.
-
(1994)
Annals of the Missouri Botanical Garden
, vol.81
, Issue.3
, pp. 484-533
-
-
Nixon, K.C.1
Crepet, W.L.2
Stevenson, D.W.3
Friis, E.M.4
-
45
-
-
0036177790
-
Seed Plant Relationships and the Systematic Position of Gnetales Based on Nuclear and Chloroplast DNA: Conflicting Data, Rooting Problems, and the Monophyly of Conifers
-
Rydin C, Kallersjo M, Friis EM. Seed Plant Relationships and the Systematic Position of Gnetales Based on Nuclear and Chloroplast DNA: Conflicting Data, Rooting Problems, and the Monophyly of Conifers. Int. J. Plant Sci. 2002, 163(2):197-214.
-
(2002)
Int. J. Plant Sci.
, vol.163
, Issue.2
, pp. 197-214
-
-
Rydin, C.1
Kallersjo, M.2
Friis, E.M.3
-
46
-
-
47649087623
-
Inference of higher-order conifer relationships from a multi-locus plastid data set
-
Rai HS, Reeves PA, Peakall R, Olmstead RG, Graham SW. Inference of higher-order conifer relationships from a multi-locus plastid data set. Botany 2008, 86:658-669.
-
(2008)
Botany
, vol.86
, pp. 658-669
-
-
Rai, H.S.1
Reeves, P.A.2
Peakall, R.3
Olmstead, R.G.4
Graham, S.W.5
-
47
-
-
67349254201
-
Loss of all plastid ndh genes in Gnetales and conifers: extent and evolutionary significance for the seed plant phylogeny
-
10.1007/s00294-009-0249-7, 19449185
-
Braukmann TWA, Kuzmina M, Stefanovic S. Loss of all plastid ndh genes in Gnetales and conifers: extent and evolutionary significance for the seed plant phylogeny. Current Genetics 2009, 55(3):323-337. 10.1007/s00294-009-0249-7, 19449185.
-
(2009)
Current Genetics
, vol.55
, Issue.3
, pp. 323-337
-
-
Braukmann, T.W.A.1
Kuzmina, M.2
Stefanovic, S.3
-
48
-
-
33748766899
-
ESTimating plant phylogeny: lessons from partitioning
-
1564041, 16776834
-
de La Torre-Bárcena JE, Egan M, Katari MS, Brenner ED, Stevenson DW, Coruzzi GM, DeSalle R. ESTimating plant phylogeny: lessons from partitioning. BMC Evol. Biol. 2006, 6:48. 1564041, 16776834.
-
(2006)
BMC Evol. Biol.
, vol.6
, pp. 48
-
-
de La Torre-Bárcena, J.E.1
Egan, M.2
Katari, M.S.3
Brenner, E.D.4
Stevenson, D.W.5
Coruzzi, G.M.6
DeSalle, R.7
-
49
-
-
66749144092
-
The Impact of Outgroup Choice and Missing Data on Major Seed Plant Phylogenetics Using Genome-Wide EST Data
-
2685480, 19503618
-
de La Torre-Bárcena JE, Kolokotronis SO, Lee EK, Stevenson DW, Brenner ED, Katari MS, Coruzzi GM, DeSalle R. The Impact of Outgroup Choice and Missing Data on Major Seed Plant Phylogenetics Using Genome-Wide EST Data. PLoS ONE 2009, 4(6):e5764. 2685480, 19503618.
-
(2009)
PLoS ONE
, vol.4
, Issue.6
-
-
de La Torre-Bárcena, J.E.1
Kolokotronis, S.O.2
Lee, E.K.3
Stevenson, D.W.4
Brenner, E.D.5
Katari, M.S.6
Coruzzi, G.M.7
DeSalle, R.8
-
50
-
-
33847212859
-
Assessing systematic error in the inference of seed plant phylogeny
-
Burleigh JG, Mathews S. Assessing systematic error in the inference of seed plant phylogeny. Int. J. Plant Sci. 2007, 168(2):125-135.
-
(2007)
Int. J. Plant Sci.
, vol.168
, Issue.2
, pp. 125-135
-
-
Burleigh, J.G.1
Mathews, S.2
-
51
-
-
34548108492
-
Chloroplast Genome (cpDNA) of Cycas taitungensis and 56 Cp Protein-coding Genes of Gnetum parvifolium: Insights into CpDNA Evolution and Phylogeny of Extant Seed Plants
-
10.1093/molbev/msm059, 17383970
-
Wu CS, Wang YN, Liu SM, Chaw SM. Chloroplast Genome (cpDNA) of Cycas taitungensis and 56 Cp Protein-coding Genes of Gnetum parvifolium: Insights into CpDNA Evolution and Phylogeny of Extant Seed Plants. Mol. Biol. Evol. 2007, 24:1366-1379. 10.1093/molbev/msm059, 17383970.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 1366-1379
-
-
Wu, C.S.1
Wang, Y.N.2
Liu, S.M.3
Chaw, S.M.4
-
52
-
-
0038632308
-
Outgroup Misplacement and Phylogenetic Inaccuracy under a Molecular Clock: A Simulation Study
-
10.1080/10635150390192771, 12746148
-
Holland BR, Penny D, Hendy MD. Outgroup Misplacement and Phylogenetic Inaccuracy under a Molecular Clock: A Simulation Study. Syst. Biol. 2003, 52(2):229-238. 10.1080/10635150390192771, 12746148.
-
(2003)
Syst. Biol.
, vol.52
, Issue.2
, pp. 229-238
-
-
Holland, B.R.1
Penny, D.2
Hendy, M.D.3
|