-
1
-
-
0000266922
-
Homoplasy excess ratios: New indices for measuring levels of homoplasy in phylogenetic systematics and a critique of the consistency index
-
ARCHIE, J. W. 1989. Homoplasy excess ratios: New indices for measuring levels of homoplasy in phylogenetic systematics and a critique of the consistency index. Syst. Zool. 38:253-269.
-
(1989)
Syst. Zool.
, vol.38
, pp. 253-269
-
-
Archie, J.W.1
-
3
-
-
0000367652
-
The limits of amino acid sequence data in angiosperm phylogenetic reconstruction
-
BREMER, K. 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42:795-803.
-
(1988)
Evolution
, vol.42
, pp. 795-803
-
-
Bremer, K.1
-
4
-
-
0029027331
-
A highly conserved nuclear gene for low-level phylogenetics: Elongation factor-la recovers morphology-based tree for heliothine moths
-
CHO, S., A. MITCHELL, J. C. REGIER, C. MITTER, R. W. POOLE, T. P. FRIEDLANDER, AND S. ZHAO. 1995. A highly conserved nuclear gene for low-level phylogenetics: Elongation factor-la recovers morphology-based tree for heliothine moths. Mol. Biol. Evol. 12: 650-656.
-
(1995)
Mol. Biol. Evol.
, vol.12
, pp. 650-656
-
-
Cho, S.1
Mitchell, A.2
Regier, J.C.3
Mitter, C.4
Poole, R.W.5
Friedlander, T.P.6
Zhao, S.7
-
6
-
-
0029096506
-
Sampling properties of DNA sequence data in phylogenetic analysis
-
CUMMINGS, M. P., S. P. OTTO, AND J. WAKELEY. 1995. Sampling properties of DNA sequence data in phylogenetic analysis.Mol. Biol. Evol. 12:814-822.
-
(1995)
Mol. Biol. Evol.
, vol.12
, pp. 814-822
-
-
Cummings, M.P.1
Otto, S.P.2
Wakeley, J.3
-
7
-
-
0000878798
-
Phylogenetic relationships of dipscales based on rbcL sequences
-
DONOGHUE, M. J., R. G. OLMSTEAD, J. F. SMITH, AND J. D. PALMER. 1992. Phylogenetic relationships of dipscales based on rbcL sequences. Ann. Missouri Bot. Garden 79:333-345.
-
(1992)
Ann. Missouri Bot. Garden
, vol.79
, pp. 333-345
-
-
Donoghue, M.J.1
Olmstead, R.G.2
Smith, J.F.3
Palmer, J.D.4
-
8
-
-
0027501821
-
Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules and morphology
-
EERNISSE, D. J., AND A. KLUGE. 1993. Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules and morphology. Mol. Biol. Evol. 10:1170-1195.
-
(1993)
Mol. Biol. Evol.
, vol.10
, pp. 1170-1195
-
-
Eernisse, D.J.1
Kluge, A.2
-
10
-
-
84963028421
-
A successive approximation approach to character weighting
-
FARRIS, J. S. 1969. A successive approximation approach to character weighting. Syst. Zool. 18:374-385.
-
(1969)
Syst. Zool.
, vol.18
, pp. 374-385
-
-
Farris, J.S.1
-
11
-
-
0001151063
-
The logical basis of phylogenetic analysis
-
(N. I. Platnick. and V. A. Funk, eds.). Columbia Press, New York
-
FARRIS, J. S. 1983. The logical basis of phylogenetic analysis. Pages 7-36 in Advances in cladistics, Volume II (N. I. Platnick. and V. A. Funk, eds.). Columbia Press, New York.
-
(1983)
Advances in Cladistics
, vol.2
, pp. 7-36
-
-
Farris, J.S.1
-
12
-
-
84983540175
-
The retention index and the rescaled consistency index
-
FARRIS, J. S. 1989. The retention index and the rescaled consistency index. Cladistics 5:417-419.
-
(1989)
Cladistics
, vol.5
, pp. 417-419
-
-
Farris, J.S.1
-
13
-
-
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 27:401-416.
-
(1978)
Syst. Zool
, vol.27
, pp. 401-416
-
-
Felsenstein, J.1
-
14
-
-
0000461280
-
Confidence limits on phylogenies: An approach using the bootstrap
-
FELSENSTEIN, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
-
(1985)
Evolution
, vol.39
, pp. 783-791
-
-
Felsenstein, J.1
-
15
-
-
0014092973
-
A method for estimating the number of invariant amino acid positions in a gene using cytochrome c as a model case
-
FITCH, W. M., AND E. MARGOLIASH. 1967. A method for estimating the number of invariant amino acid positions in a gene using cytochrome c as a model case. Biochem. Genet. 1:65-71.
-
(1967)
Biochem. Genet.
, vol.1
, pp. 65-71
-
-
Fitch, W.M.1
Margoliash, E.2
-
16
-
-
0024258114
-
Amniote phylogeny and the importance of fossils
-
GAUTHIER J., A. G. KLUGE, AND T. ROWE. 1988. Amniote phylogeny and the importance of fossils. Cladistics 4:105-209.
-
(1988)
Cladistics
, vol.4
, pp. 105-209
-
-
Gauthier, J.1
Kluge, A.G.2
Rowe, T.3
-
17
-
-
0027526039
-
Statistical tests of models of DNA substitution
-
GOLDMAN, N. 1993. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:182-198.
-
(1993)
J. Mol. Evol.
, vol.36
, pp. 182-198
-
-
Goldman, N.1
-
18
-
-
12044254698
-
Evaluating the phylogenetic utility of genes: A search for genes informative about deep divergences among vertebrates
-
GRAYBEAL, A. 1994. Evaluating the phylogenetic utility of genes: A search for genes informative about deep divergences among vertebrates. Syst. Biol. 43: 174-193.
-
(1994)
Syst. Biol.
, vol.43
, pp. 174-193
-
-
Graybeal, A.1
-
19
-
-
0029068893
-
Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites
-
GU, X., Y.-X. FU, AND W-H. LI. 1995. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol. Biol. Evol. 12: 546-557.
-
(1995)
Mol. Biol. Evol.
, vol.12
, pp. 546-557
-
-
Gu, X.1
Fu, Y.-X.2
Li, W.-H.3
-
20
-
-
0022376704
-
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
-
HASEGAWA, M., H. KISHINO, AND T. YANO. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 21:160-174.
-
(1985)
J. Mol. Evol.
, vol.21
, pp. 160-174
-
-
Hasegawa, M.1
Kishino, H.2
Yano, T.3
-
21
-
-
0002063701
-
Discriminating between phylogenetic signal and random noise in DNA sequences
-
(M. M. Miyamoto and J. Cracraft, eds). Oxford Univ. Press, New York
-
HILLIS, D. M. 1991. Discriminating between phylogenetic signal and random noise in DNA sequences. Pages 278-294 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. 278-294
-
-
Hillis, D.M.1
-
22
-
-
0029834661
-
Inferring complex phylogenies
-
HILLIS, D. M. 1996. Inferring complex phylogenies. Nature 383:130-131.
-
(1996)
Nature
, vol.383
, pp. 130-131
-
-
Hillis, D.M.1
-
23
-
-
12044255023
-
Success of phylogenetic methods in the four-taxon case
-
HUELSENBECK, J. P., AND D. M. HILLIS. 1993. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42:247-264.
-
(1993)
Syst. Biol.
, vol.42
, pp. 247-264
-
-
Huelsenbeck, J.P.1
Hillis, D.M.2
-
24
-
-
0000732090
-
Evolution of protein molecules
-
(H. N. Munro, ed.). Academic Press, New York
-
JUKES, T. H., AND C. R. CANTOR. 1969. Evolution of protein molecules. Pages 21-132 in Mammalian protein metabolism (H. N. Munro, ed.). Academic Press, New York.
-
(1969)
Mammalian Protein Metabolism
, pp. 21-132
-
-
Jukes, T.H.1
Cantor, C.R.2
-
25
-
-
0030315308
-
General inconsistency conditions for maximum parsimony: Effects of branch lengths and increasing numbers of taxa
-
KIM, J. 1996. General inconsistency conditions for maximum parsimony: Effects of branch lengths and increasing numbers of taxa. Syst. Biol. 45:363-374.
-
(1996)
Syst. Biol.
, vol.45
, pp. 363-374
-
-
Kim, J.1
-
26
-
-
0019296687
-
A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences
-
KIMURA, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
-
(1980)
J. Mol. Evol.
, vol.16
, pp. 111-120
-
-
Kimura, M.1
-
27
-
-
0024307824
-
Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order of the Hominoidea
-
KISHINO, H., AND M. HASEGAWA. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order of the Hominoidea. J. Mol. Evol. 29:170-179.
-
(1989)
J. Mol. Evol.
, vol.29
, pp. 170-179
-
-
Kishino, H.1
Hasegawa, M.2
-
28
-
-
0021277009
-
A new method for calculating evolutionary substitution rates
-
LANAVE, C., G. PREPARATA, C. SACCONE, AND G. SERIO. 1984. A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20:86-93.
-
(1984)
J. Mol. Evol.
, vol.20
, pp. 86-93
-
-
Lanave, C.1
Preparata, G.2
Saccone, C.3
Serio, G.4
-
29
-
-
0027662420
-
Species sampling has a major impact on phylogenetic inference
-
LECOINTRE, G., H. PHILIPPE, H. L VAN LÊ, AND H. LE GUYADER. 1993. Species sampling has a major impact on phylogenetic inference. Mol. Phyl. Evol. 2: 205-224.
-
(1993)
Mol. Phyl. Evol.
, vol.2
, pp. 205-224
-
-
Lecointre, G.1
Philippe, H.2
Van Lê, H.L.3
Le Guyader, H.4
-
30
-
-
0028361182
-
Recovering evolutionary trees under a more realistic model of sequence evolution
-
LOCKHART, P. J., M. A. STEEL, M. D. HENDY, AND D. PENNY. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11:605-612.
-
(1994)
Mol. Biol. Evol.
, vol.11
, pp. 605-612
-
-
Lockhart, P.J.1
Steel, M.A.2
Hendy, M.D.3
Penny, D.4
-
31
-
-
0000229302
-
Heads and tails: A chordate phylogeny
-
MAISEY, J. G. 1986. Heads and tails: A chordate phylogeny. Cladistics 2:201-256.
-
(1986)
Cladistics
, vol.2
, pp. 201-256
-
-
Maisey, J.G.1
-
32
-
-
0001911916
-
Phylogeny of early vertebrate skeletal induction and ossification patterns
-
(M. Hecht, B. Wallace, and G. T. Prance, eds.). Plenum, New York
-
MAISEY, J. G. 1988. Phylogeny of early vertebrate skeletal induction and ossification patterns. Evolutionary biology, Volume 22 (M. Hecht, B. Wallace, and G. T. Prance, eds.). Plenum, New York.
-
(1988)
Evolutionary Biology
, vol.22
-
-
Maisey, J.G.1
-
33
-
-
0029619271
-
The importance of base composition in the correct assessment of genetic distance
-
PESOLE, G., G. DELLISANTI, G. PREPARATA, AND C. SACCONE. 1995. The importance of base composition in the correct assessment of genetic distance. J. Mol. Evol. 41:1124-1127.
-
(1995)
J. Mol. Evol.
, vol.41
, pp. 1124-1127
-
-
Pesole, G.1
Dellisanti, G.2
Preparata, G.3
Saccone, C.4
-
34
-
-
0028578194
-
Can the Cambrian explosion be inferred through molecular phylogeny?
-
PHILIPPE H. A. CHENUIL, AND A. ADOUTTE. 1994. Can the Cambrian explosion be inferred through molecular phylogeny? Development (suppl.):15-25.
-
(1994)
Development
, Issue.SUPPL.
, pp. 15-25
-
-
Philippe, H.1
Chenuil, A.2
Adoutte, A.3
-
35
-
-
0025267792
-
The general stochastic model of nucleotide substitution
-
RODRÍGUEZ, F., J. L. OLIVER, A. MARÍN, AND J. R. MEDINA. 1990. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142:485-501.
-
(1990)
J. Theor. Biol.
, vol.142
, pp. 485-501
-
-
Rodríguez, F.1
Oliver, J.L.2
Marín, A.3
Medina, J.R.4
-
36
-
-
0030045281
-
Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny
-
RUSSO, C. A. M, N. TAKEZAKI, AND M. NEI. 1996. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol. Biol. Evol. 13:525-536.
-
(1996)
Mol. Biol. Evol.
, vol.13
, pp. 525-536
-
-
Russo, C.A.M.1
Takezaki, N.2
Nei, M.3
-
37
-
-
0024457184
-
DNA microenvironments and the molecular clock
-
SACCONE, C., G. PESOLE, AND G. PREPARATA. 1989. DNA microenvironments and the molecular clock. J. Mol. Evol. 29:407-411.
-
(1989)
J. Mol. Evol.
, vol.29
, pp. 407-411
-
-
Saccone, C.1
Pesole, G.2
Preparata, G.3
-
38
-
-
0025317141
-
Influence of base composition on quantitative estimates of gene evolution
-
SACCONE, C., C. LANAVE, G. PESOLE, AND G. PREPARATA. 1990. Influence of base composition on quantitative estimates of gene evolution. Methods Enzymol. 183:570-583.
-
(1990)
Methods Enzymol.
, vol.183
, pp. 570-583
-
-
Saccone, C.1
Lanave, C.2
Pesole, G.3
Preparata, G.4
-
40
-
-
0027180533
-
Confidence in evolutionary trees from biological sequence data
-
STEEL, M. A., P. J. LOCKHART, AND D. PENNY. 1993. Confidence in evolutionary trees from biological sequence data. Nature 364:440-442.
-
(1993)
Nature
, vol.364
, pp. 440-442
-
-
Steel, M.A.1
Lockhart, P.J.2
Penny, D.3
-
41
-
-
43949153645
-
Recovering a tree from the leaf colorations it generates under a Markov model
-
STEEL, M. A. 1994. Recovering a tree from the leaf colorations it generates under a Markov model. Appl. Math. Lett. 7:19-23.
-
(1994)
Appl. Math. Lett.
, vol.7
, pp. 19-23
-
-
Steel, M.A.1
-
42
-
-
0028807391
-
Among-site rate variation and phylogenetic analysis of 12S rRNA data in sigmodontine rodents
-
SULLIVAN, J., K. E. HOLSINGER, AND C. SIMON. 1995. Among-site rate variation and phylogenetic analysis of 12S rRNA data in sigmodontine rodents. Mol. Biol. Evol. 12:988-1001.
-
(1995)
Mol. Biol. Evol.
, vol.12
, pp. 988-1001
-
-
Sullivan, J.1
Holsinger, K.E.2
Simon, C.3
-
43
-
-
0029880314
-
The effect of topology on estimates of among site rate variation
-
SULLIVAN, J., K. E. HOLSINCER, AND C. SIMON. 1996. The effect of topology on estimates of among site rate variation. J. Mol. Evol. 42:308-312.
-
(1996)
J. Mol. Evol.
, vol.42
, pp. 308-312
-
-
Sullivan, J.1
Holsincer, K.E.2
Simon, C.3
-
44
-
-
85083613110
-
Uncertainty in estimating parameters of mixed-distribution models of rate heterogeneity
-
submitted to
-
SULLIVAN, J., D. L. SWOFFORD, AND G. J. P. NAYLOR. Uncertainty in estimating parameters of mixed-distribution models of rate heterogeneity. (submitted to Syst. Biol.)
-
Syst. Biol.
-
-
Sullivan, J.1
Swofford, D.L.2
Naylor, G.J.P.3
-
45
-
-
0001336205
-
Phylogenetic inference
-
(D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer Associates, 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 Associates, 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
-
46
-
-
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. Lec. Math. Life Sci. 17:57-86.
-
(1986)
Lec. Math. Life Sci.
, vol.17
, pp. 57-86
-
-
Tavaré, S.1
-
47
-
-
0001897782
-
Convergent evolution and non-parametric inferences from restriction fragment and DNA sequence data
-
(B. Weir, ed.). Marcel Dekker, New York
-
TEMPLETON, A. R. 1983. Convergent evolution and non-parametric inferences from restriction fragment and DNA sequence data. Pages 151-179 in Statistical analysis of DNA sequence data (B. Weir, ed.). Marcel Dekker, New York.
-
(1983)
Statistical Analysis of DNA Sequence Data
, pp. 151-179
-
-
Templeton, A.R.1
-
48
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice
-
THOMPSON, J. D., D. G. HIGGINS, AND T. J. GIBSON. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
49
-
-
0004066618
-
-
Ph.D. Dissertation, Massey Univ., New Zealand
-
WADDELL, P. J. 1995. Statistical methods of phylogenetic analysis, including Hadamard conjugations, LogDet transforms and maximum likelihood. Ph.D. Dissertation, Massey Univ., New Zealand.
-
(1995)
Statistical Methods of Phylogenetic Analysis, Including Hadamard Conjugations, LogDet Transforms and Maximum Likelihood
-
-
Waddell, P.J.1
-
50
-
-
0028064845
-
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
-
YANG, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J. Mol. Evol. 39: 306-314.
-
(1994)
J. Mol. Evol.
, vol.39
, pp. 306-314
-
-
Yang, Z.1
|