-
1
-
-
38849106185
-
Phylogenetic ideals and varieties for the general Markov model
-
arXiv:math.AG/0410604
-
Allman, E.S. and Rhodes, J.A. (2008) Phylogenetic ideals and varieties for the general Markov model. Adv. Appl. Math., 40 arXiv:math.AG/0410604.
-
(2008)
Adv. Appl. Math.
-
-
Allman, E.S.1
Rhodes, J.A.2
-
2
-
-
84864697376
-
Inferring species trees directly from biallelic genetic markers: Bypassing gene trees in a full coalescent analysis
-
Bryant, D. et al. (2012) Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol. Biol. Evol., 29, 1917-1932.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 1917-1932
-
-
Bryant, D.1
-
4
-
-
13244292527
-
Gene tree distributions under the coalescent process
-
Degnan, J. and Salter, L. (2005) Gene tree distributions under the coalescent process. Evolution, 59, 24-37.
-
(2005)
Evolution
, vol.59
, pp. 24-37
-
-
Degnan, J.1
Salter, L.2
-
5
-
-
77249139678
-
Fast and consistent estimation of species trees using supermatrix rooted triples
-
DeGeorgio, M. and Degnan, J. (2010) Fast and consistent estimation of species trees using supermatrix rooted triples. Mol. Biol. Evol., 27, 552-569.
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 552-569
-
-
Degeorgio, M.1
Degnan, J.2
-
6
-
-
33745627269
-
Tree construction using singular value decompsition
-
Pachter, L. and Sturmfels, B. (eds). Chap 19. Cambridge University Press, Cambridge
-
Eriksson, N. (2005) Tree construction using singular value decompsition. In: Pachter, L. and Sturmfels, B. (eds) Algebraic Statistics for Computational Biology. Chap 19. Cambridge University Press, Cambridge, pp. 347-358.
-
(2005)
Algebraic Statistics for Computational Biology
, pp. 347-358
-
-
Eriksson, N.1
-
8
-
-
77249086587
-
Bayesian inference of species trees from multilocus data
-
Heled, J. and Drummond, A. (2010) Bayesian inference of species trees from multilocus data. Mol. Biol. Evol., 27, 570-580.
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 570-580
-
-
Heled, J.1
Drummond, A.2
-
9
-
-
77958059433
-
Sources of error for species-tree estimation: Impact of mutational and coalescent effects on accuracy and implications for choosing among different methods
-
Huang, H. et al. (2010) Sources of error for species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods. Syst. Biol., 59, 573-583.
-
(2010)
Syst. Biol.
, vol.59
, pp. 573-583
-
-
Huang, H.1
-
12
-
-
0002743467
-
Exchangeability and the evolution of large populations
-
Koch, G. and Spizzichino, F. (eds). North-Holland Elsevier, Amsterdam
-
Kingman, J.F.C. (1982b) Exchangeability and the evolution of large populations. In: Koch, G. and Spizzichino, F. (eds) Exchangeability in Probability and Statistics. North-Holland Elsevier, Amsterdam, pp. 97-112.
-
(1982)
Exchangeability in Probability and Statistics
, pp. 97-112
-
-
Kingman, J.F.C.1
-
13
-
-
63549118031
-
STEM: Species tree estimation using maximum likelihood for gene trees under the coalescent
-
Kubatko, L.S. et al. (2009) STEM: species tree estimation using maximum likelihood for gene trees under the coalescent. Bioinformatics, 25, 971-973.
-
(2009)
Bioinformatics
, vol.25
, pp. 971-973
-
-
Kubatko, L.S.1
-
14
-
-
79959474470
-
Inferring species-level phylogenies and taxonomic distinctiveness using multilocus data in Sistrurus rattlesnakes
-
Kubatko, L.S. et al. (2011) Inferring species-level phylogenies and taxonomic distinctiveness using multilocus data in Sistrurus rattlesnakes. Syst. Biol., 60, 393-409.
-
(2011)
Syst. Biol.
, vol.60
, pp. 393-409
-
-
Kubatko, L.S.1
-
15
-
-
78649479141
-
Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection
-
Lam, H.M. et al. (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat. Genet., 42, 1053-1059.
-
(2010)
Nat. Genet.
, vol.42
, pp. 1053-1059
-
-
Lam, H.M.1
-
16
-
-
84896740189
-
SNPhylo: A pipeline to construct a phylogenetic tree from huge SNP data
-
Lee, T.H. et al. (2014) SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data. BMC Genomics, 15, 162.
-
(2014)
BMC Genomics
, vol.15
, pp. 162
-
-
Lee, T.H.1
-
17
-
-
34548575126
-
Species trees from gene trees: Reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions
-
Liu, L. and Pearl, D. (2007) Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol., 56, 504-514.
-
(2007)
Syst. Biol.
, vol.56
, pp. 504-514
-
-
Liu, L.1
Pearl, D.2
-
18
-
-
68049099068
-
Coalescent methods for estimating phylogenetic trees
-
Liu, L. et al. (2009a) Coalescent methods for estimating phylogenetic trees. Mol. Phylogenet. Evol., 52, 320-328.
-
(2009)
Mol. Phylogenet. Evol.
, vol.52
, pp. 320-328
-
-
Liu, L.1
-
19
-
-
70350247510
-
Maximum tree: A consistent estimator of the species tree
-
Liu, L. et al. (2009b) Maximum tree: a consistent estimator of the species tree. J. Math. Biol., 60, 95-106.
-
(2009)
J. Math. Biol.
, vol.60
, pp. 95-106
-
-
Liu, L.1
-
20
-
-
70349425459
-
Estimating species phylogenies using coalescence times among sequences
-
Liu, L. et al. (2009c) Estimating species phylogenies using coalescence times among sequences. Syst. Biol., 58, 468-477.
-
(2009)
Syst. Biol.
, vol.58
, pp. 468-477
-
-
Liu, L.1
-
21
-
-
77957686501
-
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
-
Liu, L. et al. (2010) A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol. Biol., 10, 302.
-
(2010)
BMC Evol. Biol.
, vol.10
, pp. 302
-
-
Liu, L.1
-
22
-
-
0031504952
-
Gene trees in species trees
-
Maddison, W. (1997) Gene trees in species trees. Syst. Biol., 46, 523-536.
-
(1997)
Syst. Biol.
, vol.46
, pp. 523-536
-
-
Maddison, W.1
-
23
-
-
0030928378
-
Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic treess
-
Rambaut, A. and Grassly, N.C. (1997) Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci., 13, 235-238.
-
(1997)
Comput. Appl. Biosci.
, vol.13
, pp. 235-238
-
-
Rambaut, A.1
Grassly, N.C.2
-
24
-
-
0041817551
-
Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci
-
Rannala, B. and Yang, Z. (2003) Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics, 164, 1645-1656.
-
(2003)
Genetics
, vol.164
, pp. 1645-1656
-
-
Rannala, B.1
Yang, Z.2
-
25
-
-
83655184666
-
Quartet MaxCut: A fast algorithm for amalgamating quartet trees
-
Snir, S. and Rao., S. (2012) Quartet MaxCut: a fast algorithm for amalgamating quartet trees. Mol. Phylogen. Evol., 62, 1-8.
-
(2012)
Mol. Phylogen. Evol.
, vol.62
, pp. 1-8
-
-
Snir, S.1
Rao, S.2
-
26
-
-
0029836454
-
Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies
-
Strimmer, K. and von Haeseler, A. (1996) Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol., 13, 964-969.
-
(1996)
Mol. Biol. Evol.
, vol.13
, pp. 964-969
-
-
Strimmer, K.1
Von Haeseler, A.2
-
27
-
-
0000338432
-
Bayesian probabilities and quartet puzzling
-
Strimmer, K. et al. (1997) Bayesian probabilities and quartet puzzling. Mol. Biol. Evol., 14, 210-213.
-
(1997)
Mol. Biol. Evol.
, vol.14
, pp. 210-213
-
-
Strimmer, K.1
-
28
-
-
0002671410
-
Some probabilistic and statistical problems in the analysis of DNA sequences
-
Tavare, S. (1986) Some probabilistic and statistical problems in the analysis of DNA sequences. Lect. Math. Life Sci., 17, 57-86.
-
(1986)
Lect. Math. Life Sci.
, vol.17
, pp. 57-86
-
-
Tavare, S.1
-
29
-
-
70349658769
-
Species tree inference by minimizing deep coalescences
-
Than, C. and Nakhleh, L. (2009) Species tree inference by minimizing deep coalescences. PLoS Comput. Biol., 5, e1000501.
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Than, C.1
Nakhleh, L.2
|