-
2
-
-
0032927161
-
Topological bias and inconsistency of maximum likelihood using wrong models
-
BRUNO, W. J., AND A. L. HALPERN. 1999. Topological bias and inconsistency of maximum likelihood using wrong models. Mol. Biol. Evol. 16:564-566.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 564-566
-
-
Bruno, W.J.1
Halpern, A.L.2
-
4
-
-
0028457465
-
The effects of sequence length, tree topology, and number of taxa on the performance of phylogenetic methods
-
CHARLESTON, M. A., M. D. HENDY, AND D. PENNY. 1994. The effects of sequence length, tree topology, and number of taxa on the performance of phylogenetic methods. J. Comp. Biol. 1:133-151.
-
(1994)
J. Comp. Biol.
, vol.1
, pp. 133-151
-
-
Charleston, M.A.1
Hendy, M.D.2
Penny, D.3
-
5
-
-
0030621127
-
Mass survival of birds across the Cretaceous-Tertiary boundary: Molecular evidence
-
COOPER, A., AND D. PENNY. 1997. Mass survival of birds across the Cretaceous-Tertiary boundary: Molecular evidence. Science 275:1109-1113.
-
(1997)
Science
, vol.275
, pp. 1109-1113
-
-
Cooper, A.1
Penny, D.2
-
7
-
-
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
-
8
-
-
84959798530
-
Cases in which parsimony or compatibility methods will be positively misleading
-
FELSENSTEIN, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
-
(1978)
Syst. Zool.
, vol.27
, pp. 401-410
-
-
Felsenstein, J.1
-
9
-
-
0003437299
-
-
Distributed by the author, Department of Genetics, Univ. Washington, Seattle
-
FELSENSTEIN, J. 1993. PHYLIP: Phylogeny inference package, version 3.5c. Distributed by the author, Department of Genetics, Univ. Washington, Seattle.
-
(1993)
PHYLIP: Phylogeny Inference Package, Version 3.5c
-
-
Felsenstein, J.1
-
10
-
-
0000084234
-
A framework for the quantitative study of evolutionary trees
-
HENDY, M. D., AND D. PENNY. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297-309.
-
(1989)
Syst. Zool.
, vol.38
, pp. 297-309
-
-
Hendy, M.D.1
Penny, D.2
-
12
-
-
0028362880
-
Application and accuracy of molecular phylogenies
-
HILLIS, D. M., J. P. HUELSENBECK, AND C. W. CUNNINGHAM. 1994. Application and accuracy of molecular phylogenies. Science 264:671-677.
-
(1994)
Science
, vol.264
, pp. 671-677
-
-
Hillis, D.M.1
Huelsenbeck, J.P.2
Cunningham, C.W.3
-
14
-
-
12044253704
-
Improving the accuracy of phylogenetic estimation by combining different methods
-
KIM, J. 1993. Improving the accuracy of phylogenetic estimation by combining different methods. Syst. Biol. 42:331-340.
-
(1993)
Syst. Biol.
, vol.42
, pp. 331-340
-
-
Kim, J.1
-
15
-
-
0033790132
-
Slicing hyperdimensional oranges: The geometry of phylogenetic estimation
-
KIM, J. 2000. Slicing hyperdimensional oranges: The geometry of phylogenetic estimation. Mol. Phylogenet. Evol. 17:58-75.
-
(2000)
Mol. Phylogenet. Evol.
, vol.17
, pp. 58-75
-
-
Kim, J.1
-
16
-
-
0001464973
-
Estimation of evolutionary sequences between homologous nucleotide sequences
-
KIMURA, M. 1981. Estimation of evolutionary sequences between homologous nucleotide sequences. Proc. Natl. Acad. Sci. USA 78:454-458.
-
(1981)
Proc. Natl. Acad. Sci. USA
, vol.78
, pp. 454-458
-
-
Kimura, M.1
-
17
-
-
0003496662
-
-
Pennsylvania State Univ., University Park
-
KUMAR, S., K. TAMURA, AND M. NEI. 1993. MEGA: Molecular evolutionary genetics analysis, version 1.01. Pennsylvania State Univ., University Park.
-
(1993)
MEGA: Molecular Evolutionary Genetics Analysis, Version 1.01
-
-
Kumar, S.1
Tamura, K.2
Nei, M.3
-
18
-
-
0036897677
-
Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling
-
LIN, Y. H., P. A. MCLENACHAN, A. R. GORE, M. J. PHILLIPS, R. OTA, M. D. HENDY, AND D. PENNY. 2002. Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling. Mol. Biol. Evol. 19:2060-2070.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 2060-2070
-
-
Lin, Y.H.1
McLenachan, P.A.2
Gore, A.R.3
Phillips, M.J.4
Ota, R.5
Hendy, M.D.6
Penny, D.7
-
21
-
-
0032088703
-
Finding optimal ingroup topologies and convexities when the choice of outgroups is not obvious
-
MILINKOVITCH, M. C. 1997. Finding optimal ingroup topologies and convexities when the choice of outgroups is not obvious. Mol. Phylogenet. Evol. 9:348-357.
-
(1997)
Mol. Phylogenet. Evol.
, vol.9
, pp. 348-357
-
-
Milinkovitch, M.C.1
-
22
-
-
0033084950
-
Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes
-
MINDELL, D. P., M. D. SORENSON, D. E. DIMCHEFF, M. HASEGAWA, J. C. AST, AND T. YURI. 1999. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Syst. Biol. 48:138-152.
-
(1999)
Syst. Biol.
, vol.48
, pp. 138-152
-
-
Mindell, D.P.1
Sorenson, M.D.2
Dimcheff, D.E.3
Hasegawa, M.4
Ast, J.C.5
Yuri, T.6
-
23
-
-
0007402667
-
Testing the theory of descent
-
(M. M. Miyamoto and J. Cracraft, eds.). Oxford Univ. Press, New York
-
PENNY, D., M. D. HENDY, AND M. A. STEEL. 1991. Testing the theory of descent. Pages 155-183 in Phylogenetic analysis of DNA sequences (M. M. Miyamoto and J. Cracraft, eds.). Oxford Univ. Press, New York.
-
(1991)
Phylogenetic Analysis of DNA Sequences
, pp. 155-183
-
-
Penny, D.1
Hendy, M.D.2
Steel, M.A.3
-
24
-
-
0035145114
-
Simple (wrong) models for complex trees: A case from Retroviridae
-
POSADA, D., AND K. A. CRANDALL. 2001. Simple (wrong) models for complex trees: A case from Retroviridae. Mol. Biol. Evol. 18:271-275.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 271-275
-
-
Posada, D.1
Crandall, K.A.2
-
25
-
-
0033604548
-
The earliest angiosperms: Evidence from mitochondrial, plastid and nuclear genomes
-
QUI, Y., J. LEE, F. BERNASCONI-QUADRONI, D. E. SOLTIS, P. S. SOLTIS, M. ZANIS, E. A. ZIMMER, Z. CHEN, V. SAVOLAINEN, AND M. W. CHASE. 1999. The earliest angiosperms: Evidence from mitochondrial, plastid and nuclear genomes. Nature 402:404-407.
-
(1999)
Nature
, vol.402
, pp. 404-407
-
-
Qui, Y.1
Lee, J.2
Bernasconi-Quadroni, F.3
Soltis, D.E.4
Soltis, P.S.5
Zanis, M.6
Zimmer, E.A.7
Chen, Z.8
Savolainen, V.9
Chase, M.W.10
-
26
-
-
0030928378
-
Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
-
RAMBAUT, A. E., AND N. C. GRASSLY. 1997. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 1:235-238.
-
(1997)
Comput. Appl. Biosci.
, vol.1
, pp. 235-238
-
-
Rambaut, A.E.1
Grassly, N.C.2
-
27
-
-
0000329594
-
Relative efficiencies of the Fitch-Margoliash, maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree
-
SAITOU, N., AND T. IMANISHI. 1989. Relative efficiencies of the Fitch-Margoliash, maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree. Mol. Biol. Evol. 6:514-525.
-
(1989)
Mol. Biol. Evol.
, vol.6
, pp. 514-525
-
-
Saitou, N.1
Imanishi, T.2
-
28
-
-
0027951531
-
Rooting molecular trees: Problems and strategies
-
SMITH, A. B. 1994. Rooting molecular trees: Problems and strategies. Biol. J. Linn. Soc. 51:279-292.
-
(1994)
Biol. J. Linn. Soc.
, vol.51
, pp. 279-292
-
-
Smith, A.B.1
-
29
-
-
0033604619
-
Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology
-
SOLTIS, P. S., D. E. SOLTIS, AND M. W. CHASE. 1999. Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature 402:402-404.
-
(1999)
Nature
, vol.402
, pp. 402-404
-
-
Soltis, P.S.1
Soltis, D.E.2
Chase, M.W.3
-
30
-
-
0023105557
-
Accuracy of phylogenetic trees estimated from DNA sequence data
-
SOURDIS, J., AND C. KRIMBAS. 1987. Accuracy of phylogenetic trees estimated from DNA sequence data. Mol. Biol. Evol. 4:159-166.
-
(1987)
Mol. Biol. Evol.
, vol.4
, pp. 159-166
-
-
Sourdis, J.1
Krimbas, C.2
-
33
-
-
0001336205
-
Phylogenetic inference
-
(D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer, Sunderland, Massachusetts
-
SWOFFORD, D. L., G. J. OLSEN, P. J. WADDELL, AND D. M. HILLIS. 1996. Phylogenetic inference. Pages 407-514 in Molecular systematics, 2nd edition (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer, Sunderland, Massachusetts.
-
(1996)
Molecular Systematics, 2nd Edition
, pp. 407-514
-
-
Swofford, D.L.1
Olsen, G.J.2
Waddell, P.J.3
Hillis, D.M.4
-
34
-
-
0035527406
-
Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods
-
SWOFFORD, D. L., P. J. WADDELL, J. P. HUELSENBECK, P. G. FOSTER, P. O. LEWIS, AND J. S. ROGERS. 2001. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 50:525-539.
-
(2001)
Syst. Biol.
, vol.50
, pp. 525-539
-
-
Swofford, D.L.1
Waddell, P.J.2
Huelsenbeck, J.P.3
Foster, P.G.4
Lewis, P.O.5
Rogers, J.S.6
-
35
-
-
0027215171
-
Unbiased estimation of evolutionary distance between nucleotide sequences
-
TAJIMA, F. 1993. Unbiased estimation of evolutionary distance between nucleotide sequences. Mol. Biol. Evol. 10:677-688.
-
(1993)
Mol. Biol. Evol.
, vol.10
, pp. 677-688
-
-
Tajima, F.1
-
36
-
-
0028205953
-
Relative efficiencies of the maximum-likelihood, neighbor-joining and maximum-parsimony methods when substitution rates varies with site
-
TATENO, Y., N. TAKEZAKI, AND M. NEI. 1994. Relative efficiencies of the maximum-likelihood, neighbor-joining and maximum-parsimony methods when substitution rates varies with site. Mol. Biol. Evol. 11:261-277.
-
(1994)
Mol. Biol. Evol.
, vol.11
, pp. 261-277
-
-
Tateno, Y.1
Takezaki, N.2
Nei, M.3
-
37
-
-
0028289581
-
The sampling distributions and covariance matrix of phylogenetic spectra
-
WADDELL, P. J., D. PENNY, M. D. HENDY, AND G. ARNOLD. 1994. The sampling distributions and covariance matrix of phylogenetic spectra. Mol. Biol. Evol. 11:630-642.
-
(1994)
Mol. Biol. Evol.
, vol.11
, pp. 630-642
-
-
Waddell, P.J.1
Penny, D.2
Hendy, M.D.3
Arnold, G.4
-
38
-
-
0030638573
-
How often do wrong models produce better phylogenies?
-
YANG, Z. 1997. How often do wrong models produce better phylogenies? Mol. Biol. Evol. 14:105-108.
-
(1997)
Mol. Biol. Evol.
, vol.14
, pp. 105-108
-
-
Yang, Z.1
|