-
1
-
-
65249107239
-
Simultaneous Bayesian gene tree reconstruction and reconciliation analysis
-
Akerborg, O., Sennblad, B., Arvestad, L., and Lagergren, J. 2009. Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc. Natl. Acad. Sci. U.S.A. 106, 5714-5719.
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 5714-5719
-
-
Akerborg, O.1
Sennblad, B.2
Arvestad, L.3
Lagergren, J.4
-
2
-
-
2442562450
-
Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution
-
ACM Press New York
-
Arvestad, L., Berglund, A.-C., Lagergren, J., and Sennblad, B. 2004. Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution, 326-335. Proceedings of RECOMB04. ACM Press New York
-
(2004)
Proceedings of RECOMB04
, pp. 326-335
-
-
Arvestad, L.1
Berglund, A.-C.2
Lagergren, J.3
Sennblad, B.4
-
3
-
-
70349414048
-
The gene evolution model and computing its associated probabilities
-
Proceedings of RECOMB04. ACM Press, New York. Arvestad, L., Lagergren, J., and Sennblad, B. 2009. The gene evolution model and computing its associated probabilities. J. ACM. 56, 1-44.
-
(2009)
J. ACM.
, vol.56
, pp. 1-44
-
-
Arvestad, L.1
Lagergren, J.2
Sennblad, B.3
-
4
-
-
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
-
5
-
-
27844468683
-
Reconciling a gene tree to a species tree under the duplication cost model
-
Bonizzoni, P., Della Vedova, G., and Dondi, R. 2005. Reconciling a gene tree to a species tree under the duplication cost model. Theor. Comput. Sci. 347, 36-53.
-
(2005)
Theor. Comput. Sci.
, vol.347
, pp. 36-53
-
-
Bonizzoni, P.1
Della Vedova, G.2
Dondi, R.3
-
6
-
-
70349193234
-
Locating large-scale gene duplication events through reconciled trees: Implications for identifying ancient polyploidy events in plants
-
Burleigh, J., Bansal, M., Wehe, A., and Eulenstein, O. 2009. Locating large-scale gene duplication events through reconciled trees: implications for identifying ancient polyploidy events in plants. J. Comput. Biol. 16, 1071-1083.
-
(2009)
J. Comput. Biol.
, vol.16
, pp. 1071-1083
-
-
Burleigh, J.1
Bansal, M.2
Wehe, A.3
Eulenstein, O.4
-
7
-
-
78549247493
-
IGTP: A software package for large-scale gene tree parsimony analysis
-
Chaudhary, R., Bansal, M.S., Wehe, A., et al. 2010. iGTP: a software package for large-scale gene tree parsimony analysis. BMC Bioinformatics 11, 574.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 574
-
-
Chaudhary, R.1
Bansal, M.S.2
Wehe, A.3
-
8
-
-
84877145695
-
Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence
-
Chaudhary, R., Burleigh, J.G., and Eulenstein, O. 2012. Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence. BMC Bioinformatics 13 Suppl 10, S11.
-
(2012)
BMC Bioinformatics
, vol.13
, Issue.SUPPL. 10
-
-
Chaudhary, R.1
Burleigh, J.G.2
Eulenstein, O.3
-
9
-
-
19644386079
-
Rates and patterns of gene duplication and loss in the human genome
-
Cotton, J.A., and Page, R.D.M. 2005. Rates and patterns of gene duplication and loss in the human genome. Proc. Biol. Sci. 272, 277-283.
-
(2005)
Proc. Biol. Sci.
, vol.272
, pp. 277-283
-
-
Cotton, J.A.1
Page, R.D.M.2
-
10
-
-
84863110624
-
Minimum leaf removal for reconciliation: Complexity and algorithms
-
Kärkkäinen, J., and Stoye, J., eds
-
Dondi, R., and El-Mabrouk, N. 2012. Minimum leaf removal for reconciliation: complexity and algorithms. In Kärkkäinen, J., and Stoye, J., eds. Proceedings of the 23rd Annual Symposium on Combinatorial Pattern Matching (CPM 2012). Lecture Notes in Computer Science, volume 7354, 399-412.
-
(2012)
Proceedings of the 23rd Annual Symposium on Combinatorial Pattern Matching (CPM 2012). Lecture Notes in Computer Science
, vol.7354
, pp. 399-412
-
-
Dondi, R.1
El-Mabrouk, N.2
-
11
-
-
70349820532
-
Space of gene/species tree reconciliations and parsimonious models
-
Springer Berlin
-
Springer, Berlin. Doyon, J.-P., Chauve, C., and Hamel, S. 2009. Space of gene/species tree 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
-
12
-
-
79951533304
-
An efficient method for exploring the space of gene tree/species tree reconciliations in a probabilistic framework
-
Doyon, J.-P., Hamel, S., and Chauve, C. 2010. An efficient method for exploring the space of gene tree/species tree reconciliations in a probabilistic framework. LIRMM Technical Report RR-10002.
-
(2010)
LIRMM Technical Report RR-10002
-
-
Doyon, J.-P.1
Hamel, S.2
Chauve, C.3
-
13
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar, R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
14
-
-
84885562479
-
-
Eulenstein, O., Huzurbazar, S., and Liberles, D. 2010. Reconciling phylogenetic trees, 185-206.
-
(2010)
Reconciling Phylogenetic Trees
, pp. 185-206
-
-
Eulenstein, O.1
Huzurbazar, S.2
Liberles, D.3
-
15
-
-
79956357949
-
-
John Wiley & Sons, Inc., Hoboken, NJ
-
In Huzurbazar, S., and Liberles, D., eds. Evolution after Gene Duplication. John Wiley & Sons, Inc., Hoboken, NJ.
-
Evolution after Gene Duplication
-
-
Huzurbazar, S.1
Liberles, D.2
-
16
-
-
84862977387
-
The paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes
-
Floudas, D., Binder, M., Riley, R., et al. 2012. The paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336, 1715-1719.
-
(2012)
Science
, vol.336
, pp. 1715-1719
-
-
Floudas, D.1
Binder, M.2
Riley, R.3
-
17
-
-
0035179702
-
Pattern and timing of gene duplication in animal genomes
-
Friedman, R., and Hughes, A.L. 2001. Pattern and timing of gene duplication in animal genomes. Genome Res. 11, 1842-1847.
-
(2001)
Genome Res.
, vol.11
, pp. 1842-1847
-
-
Friedman, R.1
Hughes, A.L.2
-
18
-
-
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., et al. 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
-
19
-
-
84877152040
-
Algorithms: Simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem
-
Górecki, P., and Eulenstein, O. 2012. Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem. BMC Bioinformatics 13, S14.
-
(2012)
BMC Bioinformatics
, vol.13
-
-
Górecki, P.1
Eulenstein, O.2
-
20
-
-
33746345337
-
DLS-trees: A model of evolutionary scenarios
-
Gorecki, P., and Tiuryn, J. 2006. DLS-trees: a model of evolutionary scenarios. Theor. Comput. Sci. 359, 378-399.
-
(2006)
Theor. Comput. Sci.
, vol.359
, pp. 378-399
-
-
Gorecki, P.1
Tiuryn, J.2
-
21
-
-
33847295811
-
URec: A system for unrooted reconciliation
-
Available at bioinformatics.oxfordjournals.org/content/23/4/511.abstract
-
Górecki, P., and Tiuryn, J. 2007. URec: a system for unrooted reconciliation. Bioinformatics 23, 511-512. Available at bioinformatics. oxfordjournals.org/content/23/4/511.abstract
-
(2007)
Bioinformatics
, vol.23
, pp. 511-512
-
-
Górecki, P.1
Tiuryn, J.2
-
22
-
-
84857090152
-
Maximumlikelihoodmodels and algorithms for gene tree evolution with duplications and losses
-
Available at
-
Gorecki, P., Burleigh, G., and Eulenstein, O. 2011. Maximumlikelihoodmodels and algorithms for gene tree evolution with duplications and losses. BMC Bioinformatics 12, S15. Available at: www.biomedcentral.com/ 1471-2105/12/S1/S15.
-
(2011)
BMC Bioinformatics
, vol.12
-
-
Gorecki, P.1
Burleigh, G.2
Eulenstein, O.3
-
23
-
-
68049139485
-
Estimating maximum likelihood phylogenies with PhyML
-
Guindon, S., Delsuc, F., Dufayard, J., et al. 2009. Estimating maximum likelihood phylogenies with PhyML. Methods Mol. Biol. 537, 113-137.
-
(2009)
Methods Mol. Biol.
, vol.537
, pp. 113-137
-
-
Guindon, S.1
Delsuc, F.2
Dufayard, J.3
-
24
-
-
33751381461
-
Timetree: A public knowledge-base of divergence times among organisms
-
Hedges, S.B., Dudley, J., and Kumar, S. 2006. Timetree: a public knowledge-base of divergence times among organisms. Bioinformatics 22, 2971-2972.
-
(2006)
Bioinformatics
, vol.22
, pp. 2971-2972
-
-
Hedges, S.B.1
Dudley, J.2
Kumar, S.3
-
25
-
-
33644876458
-
TreeFam: A curated database of phylogenetic trees of animal gene families
-
Li, H., Coghlan, A., Ruan, J., et al. 2006. TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res. 34, D572-D580.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Li, H.1
Coghlan, A.2
Ruan, J.3
-
26
-
-
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. 51, 570-587.
-
(2002)
Syst. Biol.
, vol.51
, pp. 570-587
-
-
Martin, A.P.1
Burg, T.M.2
-
27
-
-
12044253257
-
Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas
-
Page, R.D.M. 1994. Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Syst. Biol. 43, 58-77.
-
(1994)
Syst. Biol.
, vol.43
, pp. 58-77
-
-
Page, R.D.M.1
-
28
-
-
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
-
29
-
-
0036365666
-
Vertebrate phylogenomics: Reconciled trees and gene duplications
-
Page, R.D.M., and Cotton, J. 2002. Vertebrate phylogenomics: reconciled trees and gene duplications. Pac. Sympo. Biocomput. 536-547.
-
(2002)
Pac. Sympo. Biocomput.
, pp. 536-547
-
-
Page, R.D.M.1
Cotton, J.2
-
30
-
-
38549163152
-
TreeFam: 2008 update
-
Ruan, J., Li, H., Chen, Z., et al. 2008. TreeFam: 2008 update. Nucleic Acids Res. 36, D735-D740.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Ruan, J.1
Li, H.2
Chen, Z.3
-
31
-
-
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 Suppl. 1, S3.
-
(2007)
BMC Evol. Biol.
, vol.7
, Issue.SUPPL. 1
-
-
Sanderson, M.J.1
McMahon, M.M.2
-
32
-
-
0028287102
-
The marsupial mhc: The tammar wallaby, Macropus eugenii, contains an expressed DNA-like gene on chromosome 1
-
Slade, R.W., Hale, P.T., Francis, D.I., et al. 1994. The marsupial mhc: the tammar wallaby, Macropus eugenii, contains an expressed DNA-like gene on chromosome 1. J. Mol. Evol. 38, 496-505.
-
(1994)
J. Mol. Evol.
, vol.38
, pp. 496-505
-
-
Slade, R.W.1
Hale, P.T.2
Francis, D.I.3
-
33
-
-
0036791133
-
Natural selection of the rhodopsin gene during the adaptive radiation of East African Great Lakes cichlid fishes
-
Sugawara, T., Terai, Y., and Okada, N. 2002. Natural selection of the rhodopsin gene during the adaptive radiation of East African Great Lakes cichlid fishes. Mol. Biol. Evol. 19, 1807-1811.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 1807-1811
-
-
Sugawara, T.1
Terai, Y.2
Okada, N.3
-
34
-
-
46249126320
-
DupTree: A program for large-scale phylogenetic analyses using gene tree parsimony
-
Wehe, A., Bansal, M.S., Burleigh, G.J., et al. 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, G.J.3
-
35
-
-
80355123621
-
Rapid evolution of the mitochondrial genome in chalcidoid wasps (hymenoptera: Chalcidoidea) driven by parasitic lifestyles
-
Xiao, J.-H., Jia, J.-G., Murphy, R.W., and Huang, D.-W. 2011. Rapid evolution of the mitochondrial genome in chalcidoid wasps (hymenoptera: Chalcidoidea) driven by parasitic lifestyles. PLoS One 6, e26645.
-
(2011)
PLoS One
, vol.6
-
-
Xiao, J.-H.1
Jia, J.-G.2
Murphy, R.W.3
Huang, D.-W.4
-
36
-
-
0030762443
-
On aMirkin-Muchnik-Smith conjecture for comparingmolecular phylogenies
-
Zhang, L. 1997. On aMirkin-Muchnik-Smith conjecture for comparingmolecular phylogenies. J. Comput. Biol. 4, 177-187.
-
(1997)
J. Comput. Biol.
, vol.4
, pp. 177-187
-
-
Zhang, L.1
|