-
1
-
-
0016990971
-
The origin and evolution of protein superfamilies
-
Dayhoff MO. The origin and evolution of protein superfamilies. Fed Proc 1976, 35(10):2132-2138.
-
(1976)
Fed Proc
, vol.35
, Issue.10
, pp. 2132-2138
-
-
Dayhoff, M.O.1
-
2
-
-
78649930876
-
An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers
-
Doyon J-P, Scornavacca C, Gorbunov KY, Szöllösi G, Ranwez V, Berry V. An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers. RECOMB-CG 2010, LNCS 2010, 6398:93-108.
-
(2010)
RECOMB-CG 2010, LNCS
, vol.6398
, pp. 93-108
-
-
Doyon, J.-P.1
Scornavacca, C.2
Gorbunov, K.Y.3
Szöllösi, G.4
Ranwez, V.5
Berry, V.6
-
3
-
-
84863524200
-
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer, and loss
-
Bansal MS, Alm EJ, Kellis M. Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer, and loss. In Bioinformatics 2012, 28(12):i283-i291.
-
(2012)
In Bioinformatics
, vol.28
, Issue.12
-
-
Bansal, M.S.1
Alm, E.J.2
Kellis, M.3
-
4
-
-
2442573762
-
Simultaneous identification of duplications and lateral transfers
-
New York: ACM, Bourne PE, Gusfield D, 3622630, 23734822
-
Hallett M, Lagergren J, Tofigh A. Simultaneous identification of duplications and lateral transfers. RECOMB '04 2004, 347-356. New York: ACM, Bourne PE, Gusfield D, 3622630, 23734822.
-
(2004)
RECOMB '04
, pp. 347-356
-
-
Hallett, M.1
Lagergren, J.2
Tofigh, A.3
-
5
-
-
2442593866
-
Reconciliation problems for duplication, loss and horizontal gene transfer
-
New York, NY, USA: ACM, Bourne PE, Gusfield D
-
Górecki P. Reconciliation problems for duplication, loss and horizontal gene transfer. RECOMB 2004, 316-325. New York, NY, USA: ACM, Bourne PE, Gusfield D.
-
(2004)
RECOMB
, pp. 316-325
-
-
Górecki, P.1
-
6
-
-
77649177164
-
Jane: a new tool for the cophylogeny reconstruction problem
-
10.1186/1748-7188-5-16, 2830923, 20181081
-
Conow C, Fielder D, Ovadia Y, Libeskind-Hadas R. Jane: a new tool for the cophylogeny reconstruction problem. Algorithms Mol Biol 2010, 5:16. 10.1186/1748-7188-5-16, 2830923, 20181081.
-
(2010)
Algorithms Mol Biol
, vol.5
, pp. 16
-
-
Conow, C.1
Fielder, D.2
Ovadia, Y.3
Libeskind-Hadas, R.4
-
7
-
-
79551667938
-
Simultaneous identification of duplications and lateral gene transfers
-
Tofigh A, Hallett M, Lagergren J. Simultaneous identification of duplications and lateral gene transfers. IEEE/ACMTCBB 2011, 8(2):517-535.
-
(2011)
IEEE/ACMTCBB
, vol.8
, Issue.2
, pp. 517-535
-
-
Tofigh, A.1
Hallett, M.2
Lagergren, J.3
-
8
-
-
78650987950
-
Rapid evolutionary innovation during an archaean genetic expansion
-
10.1038/nature09649, 21170026
-
David LA, Alm EJ. Rapid evolutionary innovation during an archaean genetic expansion. Nature 2011, 469(7328):93-96. 10.1038/nature09649, 21170026.
-
(2011)
Nature
, vol.469
, Issue.7328
, pp. 93-96
-
-
David, L.A.1
Alm, E.J.2
-
9
-
-
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 A, 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.4
Matsuda, G.5
-
10
-
-
0033936591
-
Extracting species trees from complex gene trees: reconciled trees and vertebrate phylogeny
-
10.1006/mpev.1999.0676, 10631044
-
Page RD. 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.1
-
11
-
-
0034938644
-
From gene trees to species trees
-
Ma B, Li M, Zhang L. From gene trees to species trees. SIComput, AMJ 2001, 30(3):729-752.
-
(2001)
SIComput, AMJ
, vol.30
, Issue.3
, pp. 729-752
-
-
Ma, B.1
Li, M.2
Zhang, L.3
-
13
-
-
70349414048
-
The gene evolution model and computing its associated probabilities
-
Arvestad L, Lagergren J, Sennblad B. The gene evolution model and computing its associated probabilities. J ACM 2009, 56(2):1-44.
-
(2009)
J ACM
, vol.56
, Issue.2
, pp. 1-44
-
-
Arvestad, L.1
Lagergren, J.2
Sennblad, B.3
-
14
-
-
80053210637
-
Models, algorithms and programs for phylogeny reconciliation
-
10.1093/bib/bbr045, 21949266
-
Doyon J-P, Ranwez V, Daubin V, Berry V. Models, algorithms and programs for phylogeny reconciliation. Brief Bioinformatics 2011, 12(5):392-400. 10.1093/bib/bbr045, 21949266.
-
(2011)
Brief Bioinformatics
, vol.12
, Issue.5
, pp. 392-400
-
-
Doyon, J.-P.1
Ranwez, V.2
Daubin, V.3
Berry, V.4
-
15
-
-
78651294037
-
The cophylogeny reconstruction problem is NP-complete
-
Ovadia Y, Fielder D, Conow C, Libeskind-Hadas R. The cophylogeny reconstruction problem is NP-complete. Comp J Biol 2011, 18(1):59-65.
-
(2011)
Comp J Biol
, vol.18
, Issue.1
, pp. 59-65
-
-
Ovadia, Y.1
Fielder, D.2
Conow, C.3
Libeskind-Hadas, R.4
-
16
-
-
58149216660
-
On the computational complexity of the reticulate cophylogeny reconstruction problem
-
Libeskind-Hadas R, Charleston MA. On the computational complexity of the reticulate cophylogeny reconstruction problem. JCB 2009, 16(1):105-117.
-
(2009)
JCB
, vol.16
, Issue.1
, pp. 105-117
-
-
Libeskind-Hadas, R.1
Charleston, M.A.2
-
17
-
-
78649937086
-
-
Sweden: Institute of Technology
-
Tofigh A. Using Trees to Capture Reticulate Evolution, Lateral Gene Transfers and Cancer Progression. PhD thesis, Royal, KTH, 2009, Sweden: Institute of Technology.
-
(2009)
Using Trees to Capture Reticulate Evolution, Lateral Gene Transfers and Cancer Progression. PhD thesis, Royal, KTH,
-
-
Tofigh, A.1
-
18
-
-
84860135294
-
Modeling gene family evolution and reconciling phylogenetic discord
-
10.1007/978-1-61779-585-5_2, 22399454, Daubin V
-
Szo{combining double acute accent} llösi GJ, Daubin V Modeling gene family evolution and reconciling phylogenetic discord. Methods Mol Biol 2012, 856:29-51. 10.1007/978-1-61779-585-5_2, 22399454, Daubin V.
-
(2012)
Methods Mol Biol
, vol.856
, pp. 29-51
-
-
Szollösi, G.J.1
-
19
-
-
33645981936
-
A hybrid micro-macroevolutionary approach to gene tree reconstruction
-
Vernot B
-
Durand D, Halldorsson BV, Vernot B A hybrid micro-macroevolutionary approach to gene tree reconstruction. Comput J Biol 2006, 13(2):320-335. Vernot B.
-
(2006)
Comput J Biol
, vol.13
, Issue.2
, pp. 320-335
-
-
Durand, D.1
Halldorsson, B.V.2
-
20
-
-
37249034790
-
Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution
-
10.1186/gb-2007-8-7-r141, 2323230, 17634151
-
Hahn MW. Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. Genome Biol 2007, 8(7):R141. 10.1186/gb-2007-8-7-r141, 2323230, 17634151.
-
(2007)
Genome Biol
, vol.8
, Issue.7
-
-
Hahn, M.W.1
-
21
-
-
33746433923
-
Optimal gene trees from sequences and species trees using a soft interpretation of parsimony
-
Berglund-Sonnhammer AC, Steffansson P, Betts MJ, Liberles DA. Optimal gene trees from sequences and species trees using a soft interpretation of parsimony. Mol J Evol 2006, 63(2):240-250.
-
(2006)
Mol J Evol
, vol.63
, Issue.2
, pp. 240-250
-
-
Berglund-Sonnhammer, A.C.1
Steffansson, P.2
Betts, M.J.3
Liberles, D.A.4
-
22
-
-
33749574597
-
Reconciling gene tree with apparent polytomies
-
Chang W, Eulenstein O. Reconciling gene tree with apparent polytomies. COCOON, LNCS 2006, 4112:235-244.
-
(2006)
COCOON, LNCS
, vol.4112
, pp. 235-244
-
-
Chang, W.1
Eulenstein, O.2
-
23
-
-
52449122085
-
Reconciliation with non-binary species trees
-
Durand D
-
Vernot B, Stolzer M, Goldman A, Durand D Reconciliation with non-binary species trees. Comput J Biol 2008, 15:981-1006. Durand D.
-
(2008)
Comput J Biol
, vol.15
, pp. 981-1006
-
-
Vernot, B.1
Stolzer, M.2
Goldman, A.3
-
25
-
-
84883747019
-
Reconciliation of gene and species trees With Polytomies
-
1201.3995v2. [q-bio.PE]
-
Zheng Y, Wu T, Zhang L. Reconciliation of gene and species trees With Polytomies. ArXiv 2012, 1201.3995v2. [q-bio.PE].
-
(2012)
ArXiv
-
-
Zheng, Y.1
Wu, T.2
Zhang, L.3
-
26
-
-
84866665369
-
An optimal reconciliation algorithm for gene trees with polytomies
-
Berlin Heidelberg: Springer-Verlag, Tang J, Raphael B, Raphael B , Tang J
-
Lafond M, Krister Swenson M, El-Mabrouk N. An optimal reconciliation algorithm for gene trees with polytomies. WABI 2012, LNBI 7534 2012, 106-122. Berlin Heidelberg: Springer-Verlag, Tang J, Raphael B, Raphael B , Tang J .
-
(2012)
WABI 2012, LNBI 7534
, pp. 106-122
-
-
Lafond, M.1
Krister Swenson, M.2
El-Mabrouk, N.3
-
27
-
-
84866458802
-
Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees
-
Stolzer M, Lai H, Xu M, Sathaye D, Vernot B, Durand D. Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees. Bioinformatics 2012, 28:409-415.
-
(2012)
Bioinformatics
, vol.28
, pp. 409-415
-
-
Stolzer, M.1
Lai, H.2
Xu, M.3
Sathaye, D.4
Vernot, B.5
Durand, D.6
-
28
-
-
84877152040
-
Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem
-
Górecki P, Eulenstein O. Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem. Bioinformatics, BMC, 2012, 13(Suppl 10):S14.
-
(2012)
Bioinformatics, BMC,
, vol.13
, Issue.SUPPL. 10
-
-
Górecki, P.1
Eulenstein, O.2
-
29
-
-
77954843377
-
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests
-
Abby S, Tannier E, Gouy M, Daubin V. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. Bioinformatics, BMC 2010, 11:324.
-
(2010)
Bioinformatics, BMC
, vol.11
, pp. 324
-
-
Abby, S.1
Tannier, E.2
Gouy, M.3
Daubin, V.4
-
30
-
-
84859467874
-
Lateral gene transfer as a support for the tree of life
-
10.1073/pnas.1116871109, 3323970, 22416123
-
Abby S, Tannier E, Gouy M, Daubin V. Lateral gene transfer as a support for the tree of life. PNAS 2012, 109(13):4962-4967. 10.1073/pnas.1116871109, 3323970, 22416123.
-
(2012)
PNAS
, vol.109
, Issue.13
, pp. 4962-4967
-
-
Abby, S.1
Tannier, E.2
Gouy, M.3
Daubin, V.4
-
32
-
-
0037314098
-
Inferring absolute rates of evolution and divergence times in the absence of a molecular clock
-
10.1093/bioinformatics/19.2.301, 12538260
-
Sanderson MJ. inferring absolute rates of evolution and divergence times in the absence of a molecular clock. Bioinformatics 2003, 19:301-302. 10.1093/bioinformatics/19.2.301, 12538260.
-
(2003)
Bioinformatics
, vol.19
, pp. 301-302
-
-
Sanderson, M.J.1
-
34
-
-
0003657590
-
-
Redwood City: Addison-Wesley Longman Publishing Co., Inc.
-
Knuth DE. The Art of Computer Programming 1998, Redwood City: Addison-Wesley Longman Publishing Co., Inc..
-
(1998)
The Art of Computer Programming
-
-
Knuth, D.E.1
-
35
-
-
0002024701
-
On the generalized birth-and-death process
-
Kendall DG. On the generalized birth-and-death process. Ann Math Stat 1948, 19:1-15.
-
(1948)
Ann Math Stat
, vol.19
, pp. 1-15
-
-
Kendall, D.G.1
-
36
-
-
38449096427
-
A model of horizontal gene transfer and the bacterial phylogeny problem
-
10.1080/10635150701546231, 17661231
-
Galtier N. A model of horizontal gene transfer and the bacterial phylogeny problem. Syst Biol 2007, 56:633-642. 10.1080/10635150701546231, 17661231.
-
(2007)
Syst Biol
, vol.56
, pp. 633-642
-
-
Galtier, N.1
-
37
-
-
0030928378
-
Seq-gen: an application for the monte carlo simulation of dna sequence evolution along phylogenetic trees
-
Rambaut A, Grass NC. Seq-gen: an application for the monte carlo simulation of dna sequence evolution along phylogenetic trees. Bioinformatics 1997, 13(3):235-238.
-
(1997)
Bioinformatics
, vol.13
, Issue.3
, pp. 235-238
-
-
Rambaut, A.1
Grass, N.C.2
-
38
-
-
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
-
39
-
-
0019424782
-
Comparison of phylogenetic trees
-
Robinson DF, Foulds LR. Comparison of phylogenetic trees. Math Biosci 1981, 53:131-147.
-
(1981)
Math Biosci
, vol.53
, pp. 131-147
-
-
Robinson, D.F.1
Foulds, L.R.2
-
40
-
-
67649115335
-
Databases of homologous gene families for comparative genomics
-
Penel S, Arigon AM, Dufayard JF, Sertier AS, Daubin V, Duret L, Gouy M, Perriere G. Databases of homologous gene families for comparative genomics. Bioinformatics, BMC 2009, 6(Suppl10):S3.
-
(2009)
Bioinformatics, BMC
, vol.6
, Issue.SUPPL. 10
-
-
Penel, S.1
Arigon, A.M.2
Dufayard, J.F.3
Sertier, A.S.4
Daubin, V.5
Duret, L.6
Gouy, M.7
Perriere, G.8
-
41
-
-
84867904826
-
Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations
-
10.1073/pnas.1202997109, 3491530, 23043116
-
Szo{combining double acute accent} llösi GJ, Boussau B, Tannier E, Daubin V. Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations. PNAS 2012, 109(43):17513-17518. 10.1073/pnas.1202997109, 3491530, 23043116.
-
(2012)
PNAS
, vol.109
, Issue.43
, pp. 17513-17518
-
-
Szollösi, G.J.1
Boussau, B.2
Tannier, E.3
Daubin, V.4
|