-
1
-
-
0002717710
-
Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today
-
Aldous D.J. 2001. Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today. Stat. Sci. 16:23-34.
-
(2001)
Stat. Sci.
, vol.16
, pp. 23-34
-
-
Aldous, D.J.1
-
2
-
-
33750245951
-
Which random processes describe the tree of liféAlarge-scale study of phylogenetic tree imbalance
-
Blum M., Francois O. 2006. Which random processes describe the tree of liféAlarge-scale study of phylogenetic tree imbalance. Syst. Biol. 55:685-691.
-
(2006)
Syst. Biol.
, vol.55
, pp. 685-691
-
-
Blum, M.1
Francois, O.2
-
3
-
-
32144453296
-
ApTreeshape: Statistical analysis of phylogenetic tree shape
-
Bortolussi N., Durand E., Blum M., Francois O. 2006. apTreeshape: Statistical analysis of phylogenetic tree shape. Bioinformatics 22:363-364.
-
(2006)
Bioinformatics
, vol.22
, pp. 363-364
-
-
Bortolussi, N.1
Durand, E.2
Blum, M.3
Francois, O.4
-
4
-
-
0002168111
-
Review of phylogenetics: The theory and practice of phylogenetic systematics by e 0
-
Colless D. 1982. Review of phylogenetics: The theory and practice of phylogenetic systematics, by E. 0. Wiley. Syst. Zool. 31:100-104.
-
(1982)
Wiley Syst. Zool.
, vol.31
, pp. 100-104
-
-
Colless, D.1
-
5
-
-
11944265753
-
Relative symmetry of cladograms and phenograms: An experimental study
-
Colless, D. 1995. Relative symmetry of cladograms and phenograms: An experimental study. Syst. Biol. 44:102-108.
-
(1995)
Syst. Biol.
, vol.44
, pp. 102-108
-
-
Colless, D.1
-
6
-
-
84944811700
-
The use of ranks to avoid the assumption of normality implicit in the analysis of variance
-
Friedman M. 1937. The use of ranks to avoid the assumption of normality implicit in the analysis of variance. J. Am. Stat. Assoc. 32:675-701.
-
(1937)
J. Am. Stat. Assoc.
, vol.32
, pp. 675-701
-
-
Friedman, M.1
-
7
-
-
77950806408
-
New algorithms and methods to estimate maximumlikelihood phylogenies: Assessing the performance of PhyML 3.0
-
Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. 2010. New algorithms and methods to estimate maximumlikelihood phylogenies: Assessing the performance of PhyML 3.0. Syst. Biol. 59:307-321.
-
(2010)
Syst. Biol.
, vol.59
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.F.2
Lefort, V.3
Anisimova, M.4
Hordijk, W.5
Gascuel, O.6
-
8
-
-
0001230144
-
Adaptive radiation and the topology of large phylogenies
-
Guyer C., Slowinski J. 1993. Adaptive radiation and the topology of large phylogenies. Evolution 47:253-263.
-
(1993)
Evolution
, vol.47
, pp. 253-263
-
-
Guyer, C.1
Slowinski, J.2
-
10
-
-
0025924711
-
Comparative methods for explaining adaptations
-
Harvey P.H., Purvis A. 1991. Comparative methods for explaining adaptations. Nature 351:619-624.
-
(1991)
Nature
, vol.351
, pp. 619-624
-
-
Harvey, P.H.1
Purvis, A.2
-
11
-
-
0001416546
-
Patterns in tree balance among cladistic, phenetic, and randomly generated phylogenetic trees
-
Heard S. 1992. Patterns in tree balance among cladistic, phenetic, and randomly generated phylogenetic trees. Evolution 46:1818-1826.
-
(1992)
Evolution
, vol.46
, pp. 1818-1826
-
-
Heard, S.1
-
13
-
-
77958450862
-
Deep genomic-scale analyses of the Metazoa reject Coelomata: Evidence from single-And multigene families analyzed under a supertree and supermatrix paradigm
-
Holton T.A., Pisani D 2010. Deep genomic-scale analyses of the Metazoa reject Coelomata: Evidence from single-And multigene families analyzed under a supertree and supermatrix paradigm. Genome Biol. Evol. 2:310-324.
-
(2010)
Genome Biol. Evol.
, vol.2
, pp. 310-324
-
-
Holton, T.A.1
Pisani, D.2
-
15
-
-
0029821511
-
Do phylogenetic methods produce trees with biased shapes?
-
Huelsenbeck J., Kirkpatrick M 1996. Do phylogenetic methods produce trees with biased shapes? Evolution 50:1418-1424.
-
(1996)
Evolution
, vol.50
, pp. 1418-1424
-
-
Huelsenbeck, J.1
Kirkpatrick, M.2
-
16
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones D.T., Taylor W.R., Thornton J.M. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
-
(1992)
Comput. Appl. Biosci.
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
17
-
-
0004265380
-
-
In: Munro H.N., editor.Mammalian protein metabolism. New York Academic Press
-
Jukes T., Cantor C. 1969. Evolution of protein molecules. In: Munro H.N., editor.Mammalian protein metabolism.New York: Academic Press.
-
(1969)
Evolution of Protein Molecules
-
-
Jukes, T.1
Cantor, C.2
-
18
-
-
33645816587
-
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
-
Keane T., Creevey C., Pentony M., Naughton T., McLnerney J. 2006. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol. Biol. 6:29.
-
(2006)
BMC Evol. Biol.
, vol.6
, pp. 29
-
-
Keane, T.1
Creevey, C.2
Pentony, M.3
Naughton, T.4
McLnerney, J.5
-
19
-
-
0001337578
-
Searching for evolutionary patterns in the shape of a phylogenetic tree
-
Kirkpatrick M., Slatkin M. 1993. Searching for evolutionary patterns in the shape of a phylogenetic tree. Evolution 47:1171-1181.
-
(1993)
Evolution
, vol.47
, pp. 1171-1181
-
-
Kirkpatrick, M.1
Slatkin, M.2
-
20
-
-
79951569162
-
Consequences of different null models on the tree shape bias of supertree methods
-
Kupczok A. 2011. Consequences of different null models on the tree shape bias of supertree methods. Syst. Biol. 60:218-225.
-
(2011)
Syst. Biol.
, vol.60
, pp. 218-225
-
-
Kupczok, A.1
-
21
-
-
2442691520
-
ABayesian mixturemodel for across-site heterogeneities in the amino-Acid replacement process
-
Lartillot N., Philippe H. 2004.ABayesian mixturemodel for across-site heterogeneities in the amino-Acid replacement process. Mol. Biol. Evol. 21:1095-1109.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 1095-1109
-
-
Lartillot, N.1
Philippe, H.2
-
22
-
-
45849154166
-
An improved general amino acid replacement matrix
-
Le S., Gascuel O. 2008. An improved general amino acid replacement matrix. Mol. Biol. Evol. 25:1307-1320.
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 1307-1320
-
-
Le, S.1
Gascuel, O.2
-
23
-
-
0034100582
-
Distributions of cherries for two models of trees
-
McKenzie A., Steel M. 2000. Distributions of cherries for two models of trees. Math. Biosci. 164:81-92.
-
(2000)
Math. Biosci.
, vol.164
, pp. 81-92
-
-
McKenzie, A.1
Steel, M.2
-
24
-
-
0002638760
-
Inferring evolutionary process from phylogenetic tree shape
-
Mooers A., Heard S. 1997. Inferring evolutionary process from phylogenetic tree shape. Q. Rev. Biol. 72:31-54.
-
(1997)
Q. Rev. Biol.
, vol.72
, pp. 31-54
-
-
Mooers, A.1
Heard, S.2
-
25
-
-
1042304216
-
APE: Analyses of phylogenetics and evolution in R language
-
Paradis E., Claude J., Strimmer K. 2004. APE: Analyses of phylogenetics and evolution in R language. Bioinformatics 20:289-290.
-
(2004)
Bioinformatics
, vol.20
, pp. 289-290
-
-
Paradis, E.1
Claude, J.2
Strimmer, K.3
-
26
-
-
0000555301
-
Central moments and probability distribution of Colless's coefficient of tree imbalance
-
Rogers J. 1994. Central moments and probability distribution of Colless's coefficient of tree imbalance. Evolution 48:2026-2036.
-
(1994)
Evolution
, vol.48
, pp. 2026-2036
-
-
Rogers, J.1
-
27
-
-
0030336191
-
Central moments and probability distributions of three measures of phylogenetic tree imbalance
-
Rogers J. 1996. Central moments and probability distributions of three measures of phylogenetic tree imbalance. Syst. Biol. 45:99-110.
-
(1996)
Syst. Biol.
, vol.45
, pp. 99-110
-
-
Rogers, J.1
-
28
-
-
84860109324
-
MrBayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space
-
Ronquist, F., Teslenko, M., Van Der Mark, P., Ayres, D.L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M.A., Huelsenbeck, J. P. 2012. MrBayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61:539-542.
-
(2012)
Systematic Biology
, vol.61
, pp. 539-542
-
-
Ronquist, F.1
Teslenko, M.2
Van Der Mark, P.3
Ayres, D.L.4
Darling, A.5
Höhna, S.6
Larget, B.7
Liu, L.8
Suchard, M.A.9
Huelsenbeck, J.P.10
-
29
-
-
33747594798
-
Vicariant pattern and historical biogeography
-
Rosen D.E. 1978. Vicariant pattern and historical biogeography. Syst. Zool. 27:159-188.
-
(1978)
Syst. Zool.
, vol.27
, pp. 159-188
-
-
Rosen, D.E.1
-
30
-
-
0036205377
-
Treepuzzle: Maximumlikelihood phylogenetic analysis using quartets and parallel computing
-
Schmidt H. A., Strimmer K., Vingron M., von Haeseler A. 2002. TREEPUZZLE: Maximumlikelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.
-
(2002)
Bioinformatics
, vol.18
, pp. 502-504
-
-
Schmidt, H.A.1
Strimmer, K.2
Vingron, M.3
Von Haeseler, A.4
-
32
-
-
0035989047
-
Does imbalance in phylogenies reflect only bias?
-
Stam E 2002. Does imbalance in phylogenies reflect only bias? Evolution 56:1292-1295.
-
(2002)
Evolution
, vol.56
, pp. 1292-1295
-
-
Stam, E.1
-
33
-
-
14644397888
-
RAxML-III: A fast program formaximumlikelihood-based inference of large phylogenetic trees
-
Stamatakis A., Ludwig T., Meier H. 2005. RAxML-III: A fast program formaximumlikelihood-based inference of large phylogenetic trees. Bioinformatics 21:456-463.
-
(2005)
Bioinformatics
, vol.21
, pp. 456-463
-
-
Stamatakis, A.1
Ludwig, T.2
Meier, H.3
-
35
-
-
84898954238
-
-
In: Janovitz M.F., Lapointe F., McMorris F.R., Mirkin B., Roberts F.S., editors. Bioconsensus. DIMCAS series in discrete mathematics and theoretical computer science. Providence, Rhode Island: The American Mathematical Society
-
Thorley J.L., Wilkinson M. 2003. A view of supertree methods. In: Janovitz M.F., Lapointe F., McMorris F.R., Mirkin B., Roberts F.S., editors. Bioconsensus. p. 183-195. DIMCAS series in discrete mathematics and theoretical computer science. Vol. 61. Providence, Rhode Island: The American Mathematical Society.
-
(2003)
A View of Supertree Methods
, vol.61
, pp. 183-195
-
-
Thorley, J.L.1
Wilkinson, M.2
-
36
-
-
78751551151
-
Random tree-puzzle leads to the Yule-Harding distribution
-
Vinh L.S., Fuehrer A., von Haeseler A. 2011. Random tree-puzzle leads to the Yule-Harding distribution. Mol. Biol. Evol. 28:873-877.
-
(2011)
Mol. Biol. Evol.
, vol.28
, pp. 873-877
-
-
Vinh, L.S.1
Fuehrer, A.2
Von Haeseler, A.3
-
37
-
-
22844442070
-
The shape of supertrees to come: Tree shape related properties of fourteen supertree methods
-
Wilkinson M., Cotton J., Creevey C., Eulenstein O., Harris S., Lapointe F., Levasseur C., McInerney J., Pisani D., Thorley J.L. 2005. The shape of supertrees to come: Tree shape related properties of fourteen supertree methods. Syst. Biol. 54:419-431.
-
(2005)
Syst. Biol.
, vol.54
, pp. 419-431
-
-
Wilkinson, M.1
Cotton, J.2
Creevey, C.3
Eulenstein, O.4
Harris, S.5
Lapointe, F.6
Levasseur, C.7
McInerney, J.8
Pisani, D.9
Thorley, J.L.10
-
38
-
-
0001778604
-
A mathematical theory of evolution, based on the conclusions of Dr. JC Willis FRS
-
Yule G. 1924 A mathematical theory of evolution, based on the conclusions of Dr. JC Willis FRS. Philos T Roy Soc Lon. B 213: 21-87.
-
(1924)
Philos T Roy Soc Lon. B
, vol.213
, pp. 21-87
-
-
Yule, G.1
-
39
-
-
84875811879
-
Does random tree puzzle produce Yule-Harding trees in the many-Taxon limit?
-
Zhu S., Steel M. 2013 Does random tree puzzle produce Yule-Harding trees in the many-Taxon limit? Math. Biosci. 243:109-116.
-
(2013)
Math. Biosci.
, vol.243
, pp. 109-116
-
-
Zhu, S.1
Steel, M.2
|