-
1
-
-
4043184290
-
Ancestral maximum likelihood of evolutionary trees is hard
-
Addario-Berry, L., Chor, B., Hallett, M., Lagergren, J., Panconesi, A., Wareham, T., 2004. Ancestral maximum likelihood of evolutionary trees is hard. J. Bioinform. Comput. Biol. 2, 257-271.
-
(2004)
J. Bioinform. Comput. Biol.
, vol.2
, pp. 257-271
-
-
Addario-Berry, L.1
Chor, B.2
Hallett, M.3
Lagergren, J.4
Panconesi, A.5
Wareham, T.6
-
2
-
-
84972510219
-
Statistical analysis of hominid molecular evolution
-
Barry, D., Hartigan, J., 1987. Statistical analysis of hominid molecular evolution. Stat. Sci. 2, 191-210.
-
(1987)
Stat. Sci.
, vol.2
, pp. 191-210
-
-
Barry, D.1
Hartigan, J.2
-
3
-
-
43949160320
-
Branch support and tree stability
-
Bremer, K., 1994. Branch support and tree stability. Cladistics 10, 295-304.
-
(1994)
Cladistics
, vol.10
, pp. 295-304
-
-
Bremer, K.1
-
4
-
-
33845335476
-
Finding a maximum likelihood tree is hard
-
Chor, B., Tuller, T., 2006. Finding a maximum likelihood tree is hard. J. ACM 53, 722-744.
-
(2006)
J. ACM
, vol.53
, pp. 722-744
-
-
Chor, B.1
Tuller, T.2
-
5
-
-
0001650804
-
Estimation of the bracing points of a branching diffusion process
-
Edwards, A.W.F., 1970. Estimation of the bracing points of a branching diffusion process. JR. Stat. Soc. B 32, 155-174.
-
(1970)
JR. Stat. Soc. B
, vol.32
, pp. 155-174
-
-
Edwards, A.W.F.1
-
6
-
-
84959807796
-
A probability model for inferring evolutionary trees
-
Farris, J.S., 1973. A probability model for inferring evolutionary trees. Syst. Zool. 22, 250-256.
-
(1973)
Syst. Zool.
, vol.22
, pp. 250-256
-
-
Farris, J.S.1
-
7
-
-
84900543268
-
-
Phylip (phylogeny inference package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
-
Felsenstein, J., 2004. Phylip (phylogeny inference package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
-
(2004)
-
-
Felsenstein, J.1
-
8
-
-
0003081588
-
The Steiner problem in phylogeny is NP-complete
-
Foulds, L.R., Graham, R.L., 1982. The Steiner problem in phylogeny is NP-complete. Adv. Appl. Math. 3, 43-49.
-
(1982)
Adv. Appl. Math.
, vol.3
, pp. 43-49
-
-
Foulds, L.R.1
Graham, R.L.2
-
9
-
-
0002795650
-
Markov chain Monte Carlo maximum likelihood
-
Keramidas, E.M. (Ed.), Interface Foundation,Fairfax Station, VA
-
Geyer, C.J., 1991. Markov chain Monte Carlo maximum likelihood. In: Keramidas, E.M. (Ed.), Computing Science and Statistics: Proceedings of the 23rd Symposium. Interface Foundation, Fairfax Station, VA, pp. 156-163.
-
(1991)
Computing Science and Statistics: Proceedings of the 23rd Symposium
, pp. 156-163
-
-
Geyer, C.J.1
-
10
-
-
0012014083
-
Some unusual small-subunit ribosomal RNA sequences of metazoans
-
Giribet, G., Wheeler, W., 2001. Some unusual small-subunit ribosomal RNA sequences of metazoans. Am. Mus. Novit. 3337, 1-14.
-
(2001)
Am. Mus. Novit.
, vol.3337
, pp. 1-14
-
-
Giribet, G.1
Wheeler, W.2
-
11
-
-
0035855865
-
Arthropod phylogeny based on eight molecular loci and morphology
-
Giribet, G., Edgecombe, G.D., Wheeler, W.C., 2001. Arthropod phylogeny based on eight molecular loci and morphology. Nature 413, 157-161.
-
(2001)
Nature
, vol.413
, pp. 157-161
-
-
Giribet, G.1
Edgecombe, G.D.2
Wheeler, W.C.3
-
12
-
-
0020400261
-
New perspectives in the molecular biological analysis of mammalian phylogeny
-
Goodman, M., Olson, C.B., Beeber, J.E., Czelusniak, J., 1982. New perspectives in the molecular biological analysis of mammalian phylogeny. Acta Zool. Fennica 169, 19-35.
-
(1982)
Acta Zool. Fennica
, vol.169
, pp. 19-35
-
-
Goodman, M.1
Olson, C.B.2
Beeber, J.E.3
Czelusniak, J.4
-
13
-
-
0040696293
-
A Bayesian probability view of phylogenetic systematics
-
Harper, C.W., 1979. A Bayesian probability view of phylogenetic systematics. Syst. Zool. 28, 547-553.
-
(1979)
Syst. Zool.
, vol.28
, pp. 547-553
-
-
Harper, C.W.1
-
14
-
-
0022376704
-
Dating the human-ape splitting by a molecular clock of mitochondrial DNA
-
Hasegawa, M., Kashina, H., Yano, T., 1985. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22, 160-174.
-
(1985)
J. Mol. Evol.
, vol.22
, pp. 160-174
-
-
Hasegawa, M.1
Kashina, H.2
Yano, T.3
-
15
-
-
0000732090
-
Evolution of protein molecules
-
Munro, N.H. (Ed.), Academic Press, New York
-
Jukes, T.H., Cantor, C.R., 1969. Evolution of protein molecules. In: Munro, N.H. (Ed.), Mammalian Protein Metabolism. Academic Press, New York, pp. 21-132.
-
(1969)
Mammalian Protein Metabolism
, pp. 21-132
-
-
Jukes, T.H.1
Cantor, C.R.2
-
16
-
-
0032976397
-
Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees
-
Larget, B., Simon, D.L., 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16, 750-759.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 750-759
-
-
Larget, B.1
Simon, D.L.2
-
17
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J., Higgins, D.G., 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
McWilliam, H.6
Valentin, F.7
Wallace, I.M.8
Wilm, A.9
Lopez, R.10
Thompson, J.D.11
Gibson, T.J.12
Higgins, D.G.13
-
18
-
-
25844516325
-
Phylogenetic MCMC algorithms are misleading on mixtures of trees
-
Mossel, E., Vigoda, E., 2005. Phylogenetic MCMC algorithms are misleading on mixtures of trees. Science 309, 2207-2209.
-
(2005)
Science
, vol.309
, pp. 2207-2209
-
-
Mossel, E.1
Vigoda, E.2
-
19
-
-
33846880861
-
Limitations of Markov chain Monte Carlo algorithms for Bayesian inference of phylogeny
-
Mossel, E., Vigoda, E., 2006. Limitations of Markov chain Monte Carlo algorithms for Bayesian inference of phylogeny. Ann. Appl. Prob. 16, 2215-2234.
-
(2006)
Ann. Appl. Prob.
, vol.16
, pp. 2215-2234
-
-
Mossel, E.1
Vigoda, E.2
-
20
-
-
0001879933
-
Molecular studies in evolution: a source of novel statistical problems
-
Gupta, S.S., Yackel, J. (Eds.), New York, Academic Press.
-
Neyman, J., 1971. Molecular studies in evolution: a source of novel statistical problems. In: Gupta, S.S., Yackel, J. (Eds.), Statistical Decision Theory and Related Topics. New York, Academic Press. pp. 1-27.
-
(1971)
Statistical Decision Theory and Related Topics
, pp. 1-27
-
-
Neyman, J.1
-
21
-
-
0029818407
-
Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference
-
Rannala, B., Yang, Z., 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43, 304-311.
-
(1996)
J. Mol. Evol.
, vol.43
, pp. 304-311
-
-
Rannala, B.1
Yang, Z.2
-
22
-
-
33144459988
-
A short proof that phylogenetic tree reconstruction by maximum likelihood is hard
-
Roch, S., 2006. A short proof that phylogenetic tree reconstruction by maximum likelihood is hard. IEEE/ACM Trans. Comput. Biol. Bioinform. 3, 92-94.
-
(2006)
IEEE/ACM Trans. Comput. Biol. Bioinform.
, vol.3
, pp. 92-94
-
-
Roch, S.1
-
23
-
-
84900542395
-
-
MrBayes: Bayesian inference of phylogeny 3.2.1. program and documentation, available at
-
Ronquist, F., Huelsenbeck, J.P., Teslenko, M., 2011. MrBayes: Bayesian inference of phylogeny 3.2.1. program and documentation, available at http://morphbank.uuse/mrbayes/.
-
(2011)
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
Teslenko, M.3
-
24
-
-
0016424695
-
Minimal mutation trees of sequences
-
Sankoff, D.M., 1975. Minimal mutation trees of sequences. SIAM J. Appl. Math. 28, 35-42.
-
(1975)
SIAM J. Appl. Math.
, vol.28
, pp. 35-42
-
-
Sankoff, D.M.1
-
25
-
-
0000459582
-
Locating the vertices of a Steiner tree in arbitrary space
-
Sankoff, D.M., Rousseau, P., 1975. Locating the vertices of a Steiner tree in arbitrary space. Math. Program. 9, 240-246.
-
(1975)
Math. Program.
, vol.9
, pp. 240-246
-
-
Sankoff, D.M.1
Rousseau, P.2
-
26
-
-
1042290602
-
Comparative and phylogenetic analysis of developmental sequences
-
Schulmeister, S., Wheeler, W.C., 2004. Comparative and phylogenetic analysis of developmental sequences. Evol. Dev. 6, 50-57.
-
(2004)
Evol. Dev.
, vol.6
, pp. 50-57
-
-
Schulmeister, S.1
Wheeler, W.C.2
-
27
-
-
0006366832
-
Likelihood analysis of mitochondrial restriction-cleavage patterns for the human-chimparnzee-gorilla trichotomy
-
Smouse, P.E., Li, W.-H., 1987. Likelihood analysis of mitochondrial restriction-cleavage patterns for the human-chimparnzee-gorilla trichotomy. Evolution 41, 1162-1176.
-
(1987)
Evolution
, vol.41
, pp. 1162-1176
-
-
Smouse, P.E.1
Li, W.-H.2
-
28
-
-
0002671410
-
Some probabilistic and statistical problems on the analysis of DNA sequences
-
Tavaré, S., 1986. Some probabilistic and statistical problems on the analysis of DNA sequences. Lect. Math. Life Sci. 17, 57-86.
-
(1986)
Lect. Math. Life Sci.
, vol.17
, pp. 57-86
-
-
Tavaré, S.1
-
29
-
-
0026079507
-
An evolutionary model for maximum likelihood alignment of DNA sequences
-
Thorne, J.L., Kishino, H., Felsenstein, J., 1991. An evolutionary model for maximum likelihood alignment of DNA sequences. J. Mol. Evol. 33, 114-124.
-
(1991)
J. Mol. Evol.
, vol.33
, pp. 114-124
-
-
Thorne, J.L.1
Kishino, H.2
Felsenstein, J.3
-
31
-
-
84900522679
-
-
POY 5.0 beta. American Museum of Natural History
-
Varón, A., Lucaroni, N., Hong, L., Wheeler, W.C., 2013. POY 5.0 beta. American Museum of Natural History, http://research.amnh.org/scicomp/projects/poy.php.
-
(2013)
-
-
Varón, A.1
Lucaroni, N.2
Hong, L.3
Wheeler, W.C.4
-
32
-
-
0028679709
-
On the complexity of multiple sequence alignment
-
Wang, L., Jiang, T., 1994. On the complexity of multiple sequence alignment. J. Comput. Biol. 1, 337-348.
-
(1994)
J. Comput. Biol.
, vol.1
, pp. 337-348
-
-
Wang, L.1
Jiang, T.2
-
33
-
-
0011166878
-
Congruence among data sets: a Bayesian approach
-
Miyamoto, M.M., Cracraft, J. (Eds.), Oxford University Press, Oxford
-
Wheeler, W.C., 1991. Congruence among data sets: a Bayesian approach. In: Miyamoto, M.M., Cracraft, J. (Eds.), Phylogenetic Analysis of DNA Sequences. Oxford University Press, Oxford, pp. 334-346.
-
(1991)
Phylogenetic Analysis of DNA Sequences
, pp. 334-346
-
-
Wheeler, W.C.1
-
34
-
-
0027280222
-
The triangle inequality and character analysis
-
Wheeler, W.C., 1993. The triangle inequality and character analysis. Mol. Biol. Evol. 10, 707-712.
-
(1993)
Mol. Biol. Evol.
, vol.10
, pp. 707-712
-
-
Wheeler, W.C.1
-
35
-
-
0001857390
-
Optimization alignment: the end of multiple sequence alignment in phylogenetics?
-
Wheeler, W.C., 1996. Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics 12, 1-9.
-
(1996)
Cladistics
, vol.12
, pp. 1-9
-
-
Wheeler, W.C.1
-
36
-
-
0035010492
-
Homology and the optimization of DNA sequence data
-
Wheeler, W.C., 2001. Homology and the optimization of DNA sequence data. Cladistics 17, S3-S11.
-
(2001)
Cladistics
, vol.17
-
-
Wheeler, W.C.1
-
37
-
-
33645096941
-
Dynamic homology and the likelihood criterion
-
Wheeler, W.C., 2006. Dynamic homology and the likelihood criterion. Cladistics 22, 157-170.
-
(2006)
Cladistics
, vol.22
, pp. 157-170
-
-
Wheeler, W.C.1
-
38
-
-
84978072356
-
The analysis of molecular sequences in large data sets: where should we put our effort?
-
Hodkinson, T.R., Parnell, J.A.N. (Eds.), Systematics Association/Oxford University Press, Oxford
-
Wheeler, W.C., 2007. The analysis of molecular sequences in large data sets: where should we put our effort? In: Hodkinson, T.R., Parnell, J.A.N. (Eds.), Reconstructing the Tree of Life: Taxonomy and Systematics of Species Rich Taxa. Systematics Association/Oxford University Press, Oxford, pp. 113-128.
-
(2007)
Reconstructing the Tree of Life: Taxonomy and Systematics of Species Rich Taxa
, pp. 113-128
-
-
Wheeler, W.C.1
-
39
-
-
78349274449
-
Distinctions between optimal and expected support
-
Wheeler, W.C., 2010. Distinctions between optimal and expected support. Cladistics 26, 657-663.
-
(2010)
Cladistics
, vol.26
, pp. 657-663
-
-
Wheeler, W.C.1
-
40
-
-
38949213680
-
Topology-Bayes versus clade-Bayes in phylogenetic analysis
-
Wheeler, W.C., Pickett, K.M., 2008. Topology-Bayes versus clade-Bayes in phylogenetic analysis. Mol. Biol. Evol. 25, 447-453.
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 447-453
-
-
Wheeler, W.C.1
Pickett, K.M.2
|