-
1
-
-
0030253222
-
Reconstruction of ancient molecular phylogeny
-
Guigó, R., Muchnik, I., and Smith, T.F. 1996 Reconstruction of ancient molecular phylogeny. Mol Phylogenet Evol. 6, 189-213.
-
(1996)
Mol Phylogenet Evol.
, vol.6
, pp. 189-213
-
-
Guigó, R.1
Muchnik, I.2
Smith, T.F.3
-
2
-
-
0036365666
-
Vertebrate phylogenomics: Reconciled trees and gene duplications
-
Page, R. D. M. and Cotton, J. A. 2002 Vertebrate phylogenomics: reconciled trees and gene duplications. Pacific Symposium on Biocomputing 536-547.
-
(2002)
Pacific Symposium on Biocomputing
, pp. 536-547
-
-
Page, R.D.M.1
Cotton, J.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 G. W., Romero- Herrera, A. E., and Matsuda, G. 1979 Fitting the gene lineage into its species lineage: a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst Zool. 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
-
-
0031504952
-
Gene trees in species trees
-
Maddison, W. P. 1997 Gene trees in species trees. Syst Biol. 46, 523-536.
-
(1997)
Syst Biol.
, vol.46
, pp. 523-536
-
-
Maddison, W.P.1
-
5
-
-
0031110886
-
From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem
-
Page, R. D. M. and Charleston, M. A. 1997 From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Mol Phylogenet Evol. 7, 231-240.
-
(1997)
Mol Phylogenet Evol.
, vol.7
, pp. 231-240
-
-
Page, R.D.M.1
Charleston, M.A.2
-
6
-
-
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. 1997. 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, 349-362.
-
(1997)
Mol Phylogenet Evol.
, vol.8
, pp. 349-362
-
-
Slowinski, J.B.1
Knight, A.2
Rooney, A.P.3
-
7
-
-
0036699004
-
Perils of paralogy: Using HSP70 genes for inferring organismal phylogenies
-
Martin, A. P. and Burg, T. M. 2002 Perils of paralogy: using HSP70 genes for inferring organismal phylogenies. Syst Biol. 41, 570-587.
-
(2002)
Syst Biol.
, vol.41
, pp. 570-587
-
-
Martin, A.P.1
Burg, T.M.2
-
8
-
-
0033936591
-
Extracting species trees from complex gene trees: Reconciled trees and vertebrate phylogeny
-
Page, R. D. M. 2000 Extracting species trees from complex gene trees: reconciled trees and vertebrate phylogeny. Mol Phylogenet Evol. 14, 89-106.
-
(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
-
Cotton, J. A. and Page, R. D. M. 2002. Going nuclear: gene family evolution and vertebrate phylogeny reconciled. P Roy Soc Lond B. Biol. 269, 1555-1561.
-
(2002)
P Roy Soc Lond B. Biol.
, vol.269
, pp. 1555-1561
-
-
Cotton, J.A.1
Page, R.D.M.2
-
10
-
-
19944410649
-
Tangled tales from multiple markers: Reconciling conflict between phylogenies to build molecular supertrees
-
Bininda-Emonds ORP, editor. Dordrecht, Netherlands: Springer-Verlag
-
Cotton, J. A. and Page, R. D. M. 2004. Tangled tales from multiple markers: reconciling conflict between phylogenies to build molecular supertrees. In: Bininda-Emonds ORP, editor. Phylogenetic supertrees: combining information to reveal the tree of life. Dordrecht, Netherlands: Springer-Verlag. p. 107-125.
-
(2004)
Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life
, pp. 107-125
-
-
Cotton, J.A.1
Page, R.D.M.2
-
11
-
-
56549101000
-
The vestigial olfactory receptor subgenome of odontocete whales: Phylogenetic congruence between gene-tree reconciliation and supermatrix methods
-
McGowen, M. R., Clark, C., and Gatesy, J. 2008 The vestigial olfactory receptor subgenome of odontocete whales: phylogenetic congruence between gene-tree reconciliation and supermatrix methods. Syst. Biol. 57, 574-590.
-
(2008)
Syst. Biol.
, vol.57
, pp. 574-590
-
-
McGowen, M.R.1
Clark, C.2
Gatesy, J.3
-
12
-
-
34248217100
-
Inferring angiosperm phylogeny from EST data with widespread gene duplication
-
Sanderson, M. J., and McMahon, M. M. 2007 Inferring angiosperm phylogeny from EST data with widespread gene duplication. BMC Evol Biol. 7, S3.
-
(2007)
BMC Evol Biol.
, vol.7
-
-
Sanderson, M.J.1
McMahon, M.M.2
-
13
-
-
34547428923
-
Heuristics for the gene-duplication problem: A (n) speed-up for the local search
-
Research in Computational Molecular Biology - 11th Annual International Conference, RECOMB 2007, Proceedings
-
Bansal, M. S., Burleigh, J.G., Eulenstein, O., and Wehe, A. 2007 Heuristics for the gene-duplication problem: A ?(n) speed-up for the local search RECOMB 2007, LNCS 4453, 238-252. (Pubitemid 47164544)
-
(2007)
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
, vol.4453
, pp. 238-252
-
-
Bansal, M.S.1
Burleigh, J.G.2
Eulenstein, O.3
Wehe, A.4
-
14
-
-
46249126320
-
DupTree: A program for large-scale phylogenetic analyses using gene tree parsimony
-
Wehe A, Bansal MS, Burleigh JG, Eulenstein O. 2008. DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics. 24:1540-1541.
-
(2008)
Bioinformatics
, vol.24
, pp. 1540-1541
-
-
Wehe, A.1
Bansal, M.S.2
Burleigh, J.G.3
Eulenstein, O.4
-
15
-
-
0036019714
-
Uninode coding vs gene tree parsimony for phylogenetic reconstruction using duplicate genes
-
Simmons, M. P. and Freudenstein, J. V. 2002 Uninode coding vs gene tree parsimony for phylogenetic reconstruction using duplicate genes. Mol Phylogenet Evol. 23, 481-498.
-
(2002)
Mol Phylogenet Evol.
, vol.23
, pp. 481-498
-
-
Simmons, M.P.1
Freudenstein, J.V.2
-
16
-
-
1642274782
-
Gene tree parsimony vs. uninode coding for phylogenetic reconstruction
-
Cotton, J. A. and Page, R. D. M. 2003 Gene tree parsimony vs. uninode coding for phylogenetic reconstruction. Mol Phylogenet Evol. 29, 298-308.
-
(2003)
Mol Phylogenet Evol.
, vol.29
, pp. 298-308
-
-
Cotton, J.A.1
Page, R.D.M.2
-
17
-
-
22844442070
-
The shape of supertrees to come: Tree shape related properties of fourteen 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. 2005 The shape of supertrees to come: tree shape related properties of fourteen supertree methods. Syst Biol. 54, 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
-
18
-
-
69549117029
-
The frequency of polyploidy speciation in vascular plants
-
Wood, T. E., Takebayashi, N., Barker, M. S., Mayrose, I., Greenspoon, P. B., and Rieseberg, L.H. 2009 The frequency of polyploidy speciation in vascular plants. Proc. Natl. Acad. Sci. USA 106, 13875-13879.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 13875-13879
-
-
Wood, T.E.1
Takebayashi, N.2
Barker, M.S.3
Mayrose, I.4
Greenspoon, P.B.5
Rieseberg, L.H.6
-
19
-
-
17244368487
-
Modeling gene and genome duplications in eukaryotes
-
Maere, S., De Bodt, S., Raes, J., Casneuf, T., Van Montagu, M., Kuiper, M., and Van de Peer, Y. 2005 Modeling gene and genome duplications in eukaryotes. Proc Natl Acad Sci USA. 102, 5454-5459.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 5454-5459
-
-
Maere, S.1
De Bodt, S.2
Raes, J.3
Casneuf, T.4
Van Montagu, M.5
Kuiper, M.6
Van De Peer, Y.7
-
20
-
-
46249107577
-
The multiple gene duplication problem revisited
-
Bansal, M. S. and Eulenstein, O. 2008 The multiple gene duplication problem revisited. Bioinformatics. 24, i132-i138.
-
(2008)
Bioinformatics
, vol.24
-
-
Bansal, M.S.1
Eulenstein, O.2
-
21
-
-
77958042924
-
Linear-time algorithms for the multiple gene duplication problems
-
Luo, C. W., Chen, M. C., Chen, Y. C., Yang, R. W. L., Liu, H. F., and Chao, K. M. 2009 Linear-time algorithms for the multiple gene duplication problems. IEEE/ACM Transactions on Computational Biology and Bioinformatics 99, 5555.
-
(2009)
IEEE/ACM Transactions on Computational Biology and Bioinformatics
, vol.99
, pp. 5555
-
-
Luo, C.W.1
Chen, M.C.2
Chen, Y.C.3
Yang, R.W.L.4
Liu, H.F.5
Chao, K.M.6
-
23
-
-
84867451275
-
On the multiple gene duplication problem
-
ISAAC'98
-
Fellows, M., Hallet, M., and Stege, U. 1998 On the multiple gene duplication problem. ISAAC'98, LNCS 1533, 347-356.
-
(1998)
LNCS
, vol.1533
, pp. 347-356
-
-
Fellows, M.1
Hallet, M.2
Stege, U.3
-
24
-
-
70349820532
-
Space of gene/species trees reconciliations and parsimonious models
-
Doyon, J. P., Chauve, C., and Hamel, S. 2009 Space of gene/species trees reconciliations and parsimonious models. J. Comput. Biol. 16, 1399-1418.
-
(2009)
J. Comput. Biol.
, vol.16
, pp. 1399-1418
-
-
Doyon, J.P.1
Chauve, C.2
Hamel, S.3
-
25
-
-
70350218974
-
An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG III
-
APG III
-
APG III. 2009 An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG III. Bot J Linn Soc. 161, 105-121.
-
(2009)
Bot J Linn Soc.
, vol.161
, pp. 105-121
-
-
-
26
-
-
33744822985
-
Widespread genome duplications throughout the history of flowering plants
-
Cui, L., Wall, P. K., Leebens-Mack, J. H., Lindsay, B. G., Soltis, D. E., Doyle, J. J., Soltis, P. S., Carlson, J.E., Arumuganathan, K., Barakat, A., Albert, V. A., Ma, H., and dePamphilis, C. W. 2006 Widespread genome duplications throughout the history of flowering plants. Genome Res. 16, 738-749.
-
(2006)
Genome Res.
, vol.16
, pp. 738-749
-
-
Cui, L.1
Wall, P.K.2
Leebens-Mack, J.H.3
Lindsay, B.G.4
Soltis, D.E.5
Doyle, J.J.6
Soltis, P.S.7
Carlson, J.E.8
Arumuganathan, K.9
Barakat, A.10
Albert, V.A.11
Ma, H.12
Depamphilis, C.W.13
-
27
-
-
60249085527
-
Polyploidy and angiosperm diversification
-
Soltis, D. E., Albert, A. A., Leebens-Mack, J., Bell, C. D., Paterson, A. H., Zheng, C., Sankoff, D., dePamphilis, C. W., Wall, P. K., and P. S. Soltis. 2009 Polyploidy and angiosperm diversification. Am. J. Bot. 96, 336-348.
-
(2009)
Am. J. Bot.
, vol.96
, pp. 336-348
-
-
Soltis, D.E.1
Albert, A.A.2
Leebens-Mack, J.3
Bell, C.D.4
Paterson, A.H.5
Zheng, C.6
Sankoff, D.7
Depamphilis, C.W.8
Wall, P.K.9
Soltis, P.S.10
-
28
-
-
33344478092
-
Phytome: A platform for plant comparative genomics
-
Hartmann, S., Lu, D., Phillips, J., and Vision, T. J. 2006 Phytome: a platform for plant comparative genomics. Nucleic Acids Res. 34, 724-730.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 724-730
-
-
Hartmann, S.1
Lu, D.2
Phillips, J.3
Vision, T.J.4
-
29
-
-
43249090276
-
Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment?
-
Hartmann, S., and Vision, T. J. 2008. Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment? BMC Evol Biol. 8, 95.
-
(2008)
BMC Evol Biol.
, vol.8
, pp. 95
-
-
Hartmann, S.1
Vision, T.J.2
-
30
-
-
33750403801
-
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis, A. 2006 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
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones, D.T., Taylor, W.R., and Thornton, J. M. 1992 The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8, 275-282.
-
(1992)
Comput. Appl. Biosci.
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
32
-
-
33847295811
-
Urec: A system for unrooted reconciliation
-
Górecki, P. and Tiuryn, J. 2007 Urec: a system for unrooted reconciliation. Bioinformatics. 23, 511-512.
-
(2007)
Bioinformatics
, vol.23
, pp. 511-512
-
-
Górecki, P.1
Tiuryn, J.2
-
33
-
-
37249034790
-
Bias in phylogenetic tree reconciliation methods: Implications for vertebrate genome evolution
-
Hahn, M. 2007 Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. Genome Biol. 8, R141.
-
(2007)
Genome Biol.
, vol.8
-
-
Hahn, M.1
-
34
-
-
70349193234
-
Locating large-scale gene duplication events through reconciled trees: Implications for identifying ancient polyploidy in plants
-
Burleigh, J. G., Bansal, M. S., Wehe, A., and Eulenstein, O. 2009 Locating large-scale gene duplication events through reconciled trees: implications for identifying ancient polyploidy in plants. J. Comput. Biol. 16, 1071-1083.
-
(2009)
J. Comput. Biol.
, vol.16
, pp. 1071-1083
-
-
Burleigh, J.G.1
Bansal, M.S.2
Wehe, A.3
Eulenstein, O.4
-
35
-
-
37249081512
-
2/log n) speed-up of TBR heuristics for the gene-duplication problem
-
Algorithms in Bioinformatics - 7th International Workshop, WABI 2007, Proceedings
-
Bansal, M. S. and Eulenstein, O 2007. An Ω(n 2/ log n) speed-up of TBR heuristics for the gene-duplication problem. WABI 2007, LNCS 4645, 124-135. (Pubitemid 350271303)
-
(2007)
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
, vol.4645
, pp. 124-135
-
-
Bansal, M.S.1
Eulenstein, O.2
-
36
-
-
49949102302
-
The gene-duplication problem: Near-linear time algorithms for NNI based local searches
-
ISBRA 2008
-
Bansal, M. S. and Eulenstein O. 2008 The gene-duplication problem: near-linear time algorithms for NNI based local searches. ISBRA 2008, LNCS 4983, 14-25.
-
(2008)
LNCS
, vol.4983
, pp. 14-25
-
-
Bansal, M.S.1
Eulenstein, O.2
-
37
-
-
77958044378
-
Scaling the gene duplication problem towards the tree of life: Accelerating the rSPR heuristic search
-
LNCS, In press
-
Wehe, A. and Burleigh, J. G. 2010 Scaling the gene duplication problem towards the tree of life: accelerating the rSPR heuristic search. BiCob 2010, LNCS, In press.
-
(2010)
BiCob 2010
-
-
Wehe, A.1
Burleigh, J.G.2
|