-
2
-
-
49549099085
-
HapCUT: An efficient and accurate algorithm for the haplotype assembly problem
-
Analysis and Computer ScienceRoyal Institute of Technology, Stockholm
-
Analysis and Computer Science, Royal Institute of Technology, Stockholm. Bansal, V., and Bafna, V. 2008. HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics 24, i153-i159.
-
(2008)
Bioinformatics
, vol.24
-
-
Bansal, V.1
Bafna, V.2
-
3
-
-
40749139524
-
Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion
-
DOI 10.1093/bioinformatics/btn024
-
Birin, H., Gal-Or, Z., Elias, I., et al. 2008. Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion. Bioinformatics 24, 826-832. (Pubitemid 351386921)
-
(2008)
Bioinformatics
, vol.24
, Issue.6
, pp. 826-832
-
-
Birin, H.1
Gal-Or, Z.2
Elias, I.3
Tuller, T.4
-
4
-
-
0000116740
-
A method for deducing branching sequences in phylogeny
-
Camin, J., and Sokal, R. 1965. A method for deducing branching sequences in phylogeny. Evolution 19,311-326.
-
(1965)
Evolution
, vol.19
, pp. 311-326
-
-
Camin, J.1
Sokal, R.2
-
5
-
-
29144484019
-
Maximum likelihood of evolutionary trees: Hardness and approximation
-
Chor, B., and Tuller, T. 2005. Maximum likelihood of evolutionary trees: hardness and approximation. Bioinformatics 21,97-106.
-
(2005)
Bioinformatics
, vol.21
, pp. 97-106
-
-
Chor, B.1
Tuller, T.2
-
6
-
-
0003882879
-
-
American Mathematical Society Providence RI
-
Chung, F.R. 1997. Spectral Graph Theory. American Mathematical Society, Providence, RI.
-
(1997)
Spectral Graph Theory
-
-
Chung, F.R.1
-
7
-
-
42549115175
-
Fast NJ-like algorithms to deal with incomplete distance matrices
-
Criscuolo, A., and Gascuel, O. 2008. Fast NJ-like algorithms to deal with incomplete distance matrices. BMC Bioinformatics 9, 166.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 166
-
-
Criscuolo, A.1
Gascuel, O.2
-
8
-
-
34250080270
-
Laplacian eigenvalues and the maximum cut problem
-
Delorme, C., and Poljak, S. 1993. Laplacian eigenvalues and the maximum cut problem. Math. Programm. 62, 557-574.
-
(1993)
Math. Programm.
, vol.62
, pp. 557-574
-
-
Delorme, C.1
Poljak, S.2
-
9
-
-
33744914841
-
Relaxed neighbor joining: A fast distance-based phylogenetic tree construction method
-
DOI 10.1007/s00239-005-0176-2
-
Evans, J., Sheneman, L., and Foster, J. 2006. Relaxed neighbor joining: a fast distance-based phylogenetic tree construction method. J. Mol. Evol. 62, 785-792. (Pubitemid 43847228)
-
(2006)
Journal of Molecular Evolution
, vol.62
, Issue.6
, pp. 785-792
-
-
Evans, J.1
Sheneman, L.2
Foster, J.3
-
10
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
DOI 10.1007/BF01734359
-
Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368-376. (Pubitemid 11016207)
-
(1981)
Journal of Molecular Evolution
, vol.17
, Issue.6
, pp. 368-376
-
-
Felsenstein, J.1
-
11
-
-
0142074265
-
Parallel algorithms for Bayesian phylogenetic inference
-
DOI 10.1016/S0743-7315(03)00079-0
-
Feng, X., Buell, D.A., Rose, J.R., et al. 2003. Parallel algorithms for Bayesian phylogenetic inference. J. Parallel Distr. Com. 63, 707-718. (Pubitemid 37268361)
-
(2003)
Journal of Parallel and Distributed Computing
, vol.63
, Issue.7-8
, pp. 707-718
-
-
Feng, X.1
Buell, D.A.2
Rose, J.R.3
Waddell, P.J.4
-
12
-
-
0001350119
-
Algebraic connectivity of graphs
-
Fieder, M. 1973. Algebraic connectivity of graphs. Czech. Math. J. 22, 298-305.
-
(1973)
Czech. Math. J.
, vol.22
, pp. 298-305
-
-
Fieder, M.1
-
13
-
-
0003081588
-
The steiner tree problem in phylogeny is np-complete
-
Foulds, L.R., and Graham, R.L. 1982. The steiner tree problem in phylogeny is np-complete. Adv. Appl. Math. 3, 4-49.
-
(1982)
Adv. Appl. Math.
, vol.3
, pp. 4-49
-
-
Foulds, L.R.1
Graham, R.L.2
-
15
-
-
0030807655
-
BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data
-
Gascuel, O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14, 685-695. (Pubitemid 27287289)
-
(1997)
Molecular Biology and Evolution
, vol.14
, Issue.7
, pp. 685-695
-
-
Gascuel, O.1
-
16
-
-
84893574327
-
Improved approximation algorithms for maximum cut and satisfiability problems using semidefinite programming
-
Goemans, M.X., and Williamson, D.P. 1995. Improved approximation algorithms for maximum cut and satisfiability problems using semidefinite programming. J. ACM 42, 1145.
-
(1995)
J. ACM
, vol.42
, pp. 1145
-
-
Goemans, M.X.1
Williamson, D.P.2
-
18
-
-
38349072117
-
Baculovirus phylogeny based on genome rearrangements
-
Goodman, D., Ollikainen, N., and Sholley, C. 2007. Baculovirus phylogeny based on genome rearrangements. Lect. Notes Comput. Sci. 4751, 69-82.
-
(2007)
Lect. Notes Comput. Sci.
, vol.4751
, pp. 69-82
-
-
Goodman, D.1
Ollikainen, N.2
Sholley, C.3
-
19
-
-
33846785301
-
QNet: An agglomerative method for the construction of phylogenetic networks from weighted quartets
-
DOI 10.1093/molbev/msl180
-
Grünewald, S., Forslund, K., Dress, A.W., et al. 2007. QNet: An agglomerative method for the construction of phylogenetic networks from weighted quartets. Mol. Biol. Evol. 24, 532-538. (Pubitemid 46204385)
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.2
, pp. 532-538
-
-
Grunewald, S.1
Forslund, K.2
Dress, A.3
Moulton, V.4
-
20
-
-
0025299784
-
Reconstructing evolution of sequences subject to recombination using parsimony
-
DOI 10.1016/0025-5564(90)90123-G
-
Hein, J. 1990. Reconstructing evolution of sequences subject to recombination using parsimony. Math. Biosci. 98, 185-200. (Pubitemid 20171457)
-
(1990)
Mathematical Biosciences
, vol.98
, Issue.2
, pp. 185-200
-
-
Hein, J.1
-
21
-
-
0027471670
-
A heuristic method to reconstruct the history of sequences subject to recombination
-
Hein, J. 1993. A heuristic method to reconstruct the history of sequences subject to recombination. J. Mol. Evol. 36, 396-405. (Pubitemid 23121907)
-
(1993)
Journal of Molecular Evolution
, vol.36
, Issue.4
, pp. 396-405
-
-
Hein, J.1
-
22
-
-
35348927445
-
Baculovirus phylogeny and evolution
-
DOI 10.2174/138945007782151306
-
Herniou, E.A., and Jehle, J.A. 2007. Baculovirus phylogeny and evolution. Curr. Drug Targets 8, 1043-1050. (Pubitemid 47578132)
-
(2007)
Current Drug Targets
, vol.8
, Issue.10
, pp. 1043-1050
-
-
Herniou, E.A.1
Jehle, J.A.2
-
23
-
-
0034864707
-
Use of whole genome sequence data to infer baculovirus phylogeny
-
DOI 10.1128/JVI.75.17.8117-8126.2001
-
Herniou, E.A., Luque, T., Chen, X., et al. 2001. Use of whole genome sequence data to infer baculovirus phylogeny. J. Virol. 75, 8117-8126. (Pubitemid 32743684)
-
(2001)
Journal of Virology
, vol.75
, Issue.17
, pp. 8117-8126
-
-
Herniou, E.A.1
Luque, T.2
Chen, X.3
Vlak, J.M.4
Winstanley, D.5
Cory, J.S.6
O'Reilly, D.R.7
-
24
-
-
0037209075
-
The Genome Sequence and Evolution of Baculoviruses
-
DOI 10.1146/annurev.ento.48.091801.112756
-
Herniou, E.A., Olszewski, J.A., Cory, J.S., et al. 2003. The genome sequence and evolution of baculoviruses. Annu. Rev. Entomol. 48, 211-234. (Pubitemid 37365392)
-
(2003)
Annual Review of Entomology
, vol.48
, pp. 211-234
-
-
Herniou, E.A.1
Olszewski, J.A.2
Cory, J.S.3
O'Reilly, D.R.4
-
25
-
-
0037379673
-
Phylogeny estimation: Traditional and Bayesian approaches
-
DOI 10.1038/nrg1044
-
Holder, M., and Lewis, P. 2003. Phylogeny estimation: traditional and Bayesian approaches. Nat. Rev. Genet. 4, 275-284. (Pubitemid 36389532)
-
(2003)
Nature Reviews Genetics
, vol.4
, Issue.4
, pp. 275-284
-
-
Holder, M.1
Lewis, P.O.2
-
26
-
-
0036857358
-
QuickTree: Building huge neighbour-joining trees of protein sequences
-
Howe, K., Bateman, A., and Durbin, R. 2002. QuickTree: building huge neighbor-joining trees of protein sequences. Bioinformatics 18, 1546-1547. (Pubitemid 35422615)
-
(2002)
Bioinformatics
, vol.18
, Issue.11
, pp. 1546-1547
-
-
Howe, K.1
Bateman, A.2
Durbin, R.3
-
27
-
-
0034849408
-
MRBAYES: Bayesian inference of phylogenetic trees
-
Huelsenbeck, J.P., and Ronquist, F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755. (Pubitemid 32851390)
-
(2001)
Bioinformatics
, vol.17
, Issue.8
, pp. 754-755
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
-
28
-
-
32844463672
-
Molecular identification and phylogenetic analysis of baculoviruses from Lepidoptera
-
DOI 10.1016/j.virol.2005.10.032, PII S0042682205007270
-
Jehle, J.A., Lange, M., Wang, H.L., et al. 2006. Molecular identification and phylogenetic analysis of baculoviruses from Lepidoptera virology. Virology 346, 180-193. (Pubitemid 43254709)
-
(2006)
Virology
, vol.346
, Issue.1
, pp. 180-193
-
-
Jehle, J.A.1
Lange, M.2
Wang, H.3
Hu, Z.4
Wang, Y.5
Hauschild, R.6
-
29
-
-
33750418625
-
Maximum likelihood of phylogenetic networks
-
DOI 10.1093/bioinformatics/btl452
-
Jin, G., Nakhleh, L., Snir, S., et al. 2006. Maximum likelihood of phylogenetic networks. Bioinformatics 22, 2604-2611. (Pubitemid 44642598)
-
(2006)
Bioinformatics
, vol.22
, Issue.21
, pp. 2604-2611
-
-
Jin, G.1
Nakhleh, L.2
Snir, S.3
Tuller, T.4
-
30
-
-
16344387501
-
DPRml: Distributed phylogeny reconstruction by maximum likelihood
-
DOI 10.1093/bioinformatics/bti100
-
Keane, T.M., Naughton, T.J., Travers, S.A., et al. 2005. DPRml: distributed phylogeny reconstruction by maximum likelihood. Bioinformatics 21, 969-974. (Pubitemid 40467917)
-
(2005)
Bioinformatics
, vol.21
, Issue.7
, pp. 969-974
-
-
Keane, T.M.1
Naughton, T.J.2
Travers, S.A.A.3
McInerney, J.O.4
McCormack, G.P.5
-
31
-
-
0015059567
-
Phylogenetic analysis: Concepts and methods
-
Kidd, K.K., and Sgaramella-Zonta, L.A. 1971. Phylogenetic analysis: concepts and methods. Am. J. Hum. Genet. 23, 235-252.
-
(1971)
Am. J. Hum. Genet.
, vol.23
, pp. 235-252
-
-
Kidd, K.K.1
Sgaramella-Zonta, L.A.2
-
32
-
-
0029917260
-
A stepwise algorithm for finding minimum evolution trees
-
Kumar, S. 1996. A stepwise algorithm for finding minimum evolution trees. Mol. Biol. Evol. 13, 584-593. (Pubitemid 26094319)
-
(1996)
Molecular Biology and Evolution
, vol.13
, Issue.4
, pp. 584-593
-
-
Kumar, S.1
-
33
-
-
0034548435
-
Efficiency of the neighbor-joining method in reconstructing deep and shallow evolutionary relationships in large phylogenies
-
Kumar, S., and Gadagkar, S.R. 2000. Efficiency of the neighbor-joining method in reconstructing deep and shallow evolutionary relationship in large phylogenies. J. Mol. Evol. 51, 544-553. (Pubitemid 32001973)
-
(2000)
Journal of Molecular Evolution
, vol.51
, Issue.6
, pp. 544-553
-
-
Kumar, S.1
Gadagkar, S.R.2
-
34
-
-
3042513497
-
Towards a molecular identification and classification system of lepidopteran-specific baculoviruses
-
DOI 10.1016/j.virol.2004.04.023, PII S0042682204002867
-
Lange, M., Wang, H.L., Zhihong, H., et al. 2004. Towards a molecular identification and classification system of lepidopteran-specific baculoviruses. Virology 325, 36-47. (Pubitemid 38844768)
-
(2004)
Virology
, vol.325
, Issue.1
, pp. 36-47
-
-
Lange, M.1
Wang, H.2
Zhihong, H.3
Jehle, J.A.4
-
35
-
-
0032976397
-
Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees
-
Larget, B., and Simon, D. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16, 750-759. (Pubitemid 29260829)
-
(1999)
Molecular Biology and Evolution
, vol.16
, Issue.6
, pp. 750-759
-
-
Larget, B.1
Simon, D.L.2
-
36
-
-
2942693569
-
Sequence and organization of the Neodiprion lecontei nucleopolyhedrovirus genome
-
DOI 10.1128/JVI.78.13.7023-7035.2004
-
Lauzon, H.A.M., Lucarotti, C.J., Krell, P.J., et al. 2004. Sequence and organization of the Neodiprion lecontei nu-cleopolyhedrovirus genome. J. Virol. 78, 7023-7035. (Pubitemid 38781541)
-
(2004)
Journal of Virology
, vol.78
, Issue.13
, pp. 7023-7035
-
-
Lauzon, H.A.M.1
Lucarotti, C.J.2
Krell, P.J.3
Feng, Q.4
Retnakaran, A.5
Arif, B.M.6
-
37
-
-
0032620819
-
Derandomizing approximation algorithms based on semidefinite programming
-
Mahajan, S., and Ramesh, H. 1999. Derandomizing approximation algorithms based on semidefinite programming. SIAM J. Comput. 28, 1641-1663. (Pubitemid 129304146)
-
(1999)
SIAM Journal on Computing
, vol.28
, Issue.5
, pp. 1641-1663
-
-
Mahajan, S.1
Ramesh, H.2
-
38
-
-
32144447594
-
Recrafting the neighbor-joining method
-
Mailund, T., Brodal, G.S., Fagerberg, R., et al. 2006. Recrafting the neighbor-joining method. BMC Bioinformatics 7, 29.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 29
-
-
Mailund, T.1
Brodal, G.S.2
Fagerberg, R.3
-
40
-
-
33846691679
-
Phylogeny reconstruction: Increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates
-
DOI 10.1093/bioinformatics/btl304
-
Ninio, M., Privman, E., Pupko, T., et al. 2007. Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates. Bioinformatics 23, e136-e141. (Pubitemid 46189648)
-
(2007)
Bioinformatics
, vol.23
, Issue.2
-
-
Ninio, M.1
Privman, E.2
Pupko, T.3
Friedman, N.4
-
41
-
-
0019424782
-
Comparison of phylogenetic trees
-
DOI 10.1016/0025-5564(81)90043-2
-
Robinson, D.F., and Foulds, L.R. 1981. Comparison of phylogenetic trees. Math. Biosci. 53, 131-147. (Pubitemid 11129084)
-
(1981)
Mathematical Biosciences
, vol.53
, Issue.1-2
, pp. 131-147
-
-
Robinson, D.F.1
Foulds, L.R.2
-
42
-
-
0022761960
-
Polyhedrin structure
-
Rohrmann, G.F. 1986. Polyhedrin structure. J. Gen. Virol. 67, 1499-1513.
-
(1986)
J. Gen. Virol.
, vol.67
, pp. 1499-1513
-
-
Rohrmann, G.F.1
-
43
-
-
0034882680
-
Traditional phylogenetic reconstruction methods reconstruct shallow and deep evolutionary relationships equally well [1]
-
Rosenberg, M.S., and Kumar, S. 2001. Traditional phylogenetic reconstruction methods reconstruct shallow and deep evolutionary relationship equally well. Mol. Biol. Evol. 18, 1823-1827. (Pubitemid 32776932)
-
(2001)
Molecular Biology and Evolution
, vol.18
, Issue.9
, pp. 1823-1827
-
-
Rosenberg, M.S.1
Kumar, S.2
-
44
-
-
0027185401
-
Theoretical foundation of the minimum-evolution method of phylogenetic inference
-
Rzhetsky, A., and Nei, M. 2003. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol. Biol. Evol. 10, 1073-1095.
-
(2003)
Mol. Biol. Evol.
, vol.10
, pp. 1073-1095
-
-
Rzhetsky, A.1
Nei, M.2
-
45
-
-
0022833247
-
The number of nucleotides required to determine the branching order of three species with special reference to the human-chimpanzee-gorilla divergence
-
Saitou, N., and Nei, M. 1986. The number of nucleotides required to determine the branching order of three species with special reference to the human-chimpanzee-gorilla divergence. J. Mol. Evol. 24, 189-204.
-
(1986)
J. Mol. Evol.
, vol.24
, pp. 189-204
-
-
Saitou, N.1
Nei, M.2
-
46
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou, N., and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
-
(1987)
Mol. Biol. Evol.
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
47
-
-
0034244751
-
Normalized cuts and image segmentation
-
Shi, J., and Malik, J. 2000. Normalized cuts and image segmentation. IEEE Trans. Pattern Anal. 22, 888-905.
-
(2000)
IEEE Trans. Pattern Anal.
, vol.22
, pp. 888-905
-
-
Shi, J.1
Malik, J.2
-
48
-
-
0032900532
-
Genome phylogeny based on gene content
-
DOI 10.1038/5052
-
Snel, B., Bork, P., and Huynen, M.A. 1999. Genome phylogeny based on gene content. Nat. Genet. 21, 108-110. (Pubitemid 29036294)
-
(1999)
Nature Genetics
, vol.21
, Issue.1
, pp. 108-110
-
-
Snel, B.1
Bork, P.2
Huynen, M.A.3
-
50
-
-
0024114801
-
A note on the neighbor-joining algorithm of Saitou and Nei, the neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Studier, J.A., and Keppler, K.J. 1988. A note on the neighbor-joining algorithm of Saitou and Nei, The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 5, 729-731.
-
(1988)
Mol. Biol. Evol.
, vol.5
, pp. 729-731
-
-
Studier, J.A.1
Keppler, K.J.2
-
51
-
-
0033854992
-
Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used
-
Takahashi, K., and Nei, M. 2000. Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol. Biol. Evol. 17, 1251-1258. (Pubitemid 30617152)
-
(2000)
Molecular Biology and Evolution
, vol.17
, Issue.8
, pp. 1251-1258
-
-
Takahashi, K.1
Nei, M.2
-
52
-
-
0030749810
-
Bayesian phylogenetic inference using DNA sequences: A Markov Chain Monte Carlo method
-
Yang, Z.H., and Rannala, B. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol. Biol. Evol. 14, 717-724. (Pubitemid 27287292)
-
(1997)
Molecular Biology and Evolution
, vol.14
, Issue.7
, pp. 717-724
-
-
Yang, Z.1
Rannala, B.2
-
53
-
-
0027665269
-
Phylogenetic interrelationships among baculoviruses: Evolutionary rates and host associations
-
DOI 10.1006/jipa.1993.1090
-
Zanotto, P.M., Kessing, B.D., and Maruniak, J.E. 1993. Phylogenetic interrelationships among baculoviruses: evolutionary rates and host associations. J. Invertebr. Pathol. 62, 147-164. (Pubitemid 223036689)
-
(1993)
Journal of Invertebrate Pathology
, vol.62
, Issue.2
, pp. 147-164
-
-
Zanotto, P.M.D.A.1
Kessing, B.D.2
Maruniak, J.E.3
|