-
1
-
-
0016355478
-
A new look at the statistical model identification
-
Akaike H. A new look at the statistical model identification. IEEE Trans. Automat. Contr. 1974, 19:716-723.
-
(1974)
IEEE Trans. Automat. Contr.
, vol.19
, pp. 716-723
-
-
Akaike, H.1
-
2
-
-
0031253343
-
Investigating phylogenetic relationships within the Apicomplexa using sequence data: the search for homology
-
Barta J.R. Investigating phylogenetic relationships within the Apicomplexa using sequence data: the search for homology. Methods 1997, 13:81-88.
-
(1997)
Methods
, vol.13
, pp. 81-88
-
-
Barta, J.R.1
-
3
-
-
0000367652
-
The limits of amino acid sequence data in angiosperm phylogenetic reconstruction
-
Bremer K. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 1988, 42:795-803.
-
(1988)
Evolution
, vol.42
, pp. 795-803
-
-
Bremer, K.1
-
4
-
-
0001762078
-
Uninformative bootstrapping
-
Carpenter J.M. Uninformative bootstrapping. Cladistics 1996, 12:177-181.
-
(1996)
Cladistics
, vol.12
, pp. 177-181
-
-
Carpenter, J.M.1
-
5
-
-
77954521496
-
Phylogeny of Celastraceae subfamily Salacioideae and tribe Lophopetaleae inferred from morphological characters and nuclear and plastid genes
-
Coughenour J.M., Simmons M.P., Lombardi J.A., Cappa J.J. Phylogeny of Celastraceae subfamily Salacioideae and tribe Lophopetaleae inferred from morphological characters and nuclear and plastid genes. Syst. Bot. 2010, 35:358-366.
-
(2010)
Syst. Bot.
, vol.35
, pp. 358-366
-
-
Coughenour, J.M.1
Simmons, M.P.2
Lombardi, J.A.3
Cappa, J.J.4
-
6
-
-
79955076551
-
Phylogeny of Celastraceae subfamily Hippocrateoideae inferred from morphological characters and nuclear and plastid genes
-
Coughenour J.M., Simmons M.P., Lombardi J.A., Yakobson K., Archer R.H. Phylogeny of Celastraceae subfamily Hippocrateoideae inferred from morphological characters and nuclear and plastid genes. Mol. Phylogenet. Evol. 2011, 59:320-330.
-
(2011)
Mol. Phylogenet. Evol.
, vol.59
, pp. 320-330
-
-
Coughenour, J.M.1
Simmons, M.P.2
Lombardi, J.A.3
Yakobson, K.4
Archer, R.H.5
-
7
-
-
72649096546
-
Molecular phylogenetics, temporal diversification, and principles of evolution in the mustard family (Brassicaceae)
-
Couvreur T.L.P., Franzke A., Al-Shehbaz I.A., Bakker F.T., Koch M.A., Mummenhoff K. Molecular phylogenetics, temporal diversification, and principles of evolution in the mustard family (Brassicaceae). Mol. Biol. Evol. 2010, 27:55-71.
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 55-71
-
-
Couvreur, T.L.P.1
Franzke, A.2
Al-Shehbaz, I.A.3
Bakker, F.T.4
Koch, M.A.5
Mummenhoff, K.6
-
8
-
-
33751012343
-
The limits of conventional cladistic analysis
-
Oxford University Press, Oxford, V.A. Albert (Ed.)
-
Davis J.I., Nixon K.C., Little D.P. The limits of conventional cladistic analysis. Parsimony, Phylogeny, and Genomics 2005, 119-147. Oxford University Press, Oxford. V.A. Albert (Ed.).
-
(2005)
Parsimony, Phylogeny, and Genomics
, pp. 119-147
-
-
Davis, J.I.1
Nixon, K.C.2
Little, D.P.3
-
9
-
-
0034350376
-
A simulation study of reduced tree-search effort in bootstrap resampling analysis
-
DeBry R.W., Olmstead R.G. A simulation study of reduced tree-search effort in bootstrap resampling analysis. Syst. Biol. 2000, 49:171-179.
-
(2000)
Syst. Biol.
, vol.49
, pp. 171-179
-
-
DeBry, R.W.1
Olmstead, R.G.2
-
10
-
-
74949137624
-
Patterns of macroevolution among primates inferred from a supermatrix of mitochondrial and nuclear DNA
-
Fabre P.-H., Rodrigues A., Douzery E.J.P. Patterns of macroevolution among primates inferred from a supermatrix of mitochondrial and nuclear DNA. Mol. Phylogenet. Evol. 2009, 53:808-825.
-
(2009)
Mol. Phylogenet. Evol.
, vol.53
, pp. 808-825
-
-
Fabre, P.-H.1
Rodrigues, A.2
Douzery, E.J.P.3
-
11
-
-
84959743928
-
Methods for computing Wagner trees
-
Farris J.S. Methods for computing Wagner trees. Syst. Zool. 1970, 19:83-92.
-
(1970)
Syst. Zool.
, vol.19
, pp. 83-92
-
-
Farris, J.S.1
-
12
-
-
84983540175
-
The retention index and the rescaled consistency index
-
Farris J.S. The retention index and the rescaled consistency index. Cladistics 1989, 5:417-419.
-
(1989)
Cladistics
, vol.5
, pp. 417-419
-
-
Farris, J.S.1
-
13
-
-
0030417648
-
Parsimony jackknifing outperforms neighbor-joining
-
Farris J.S., Albert V.A., Källersjö M., Lipscomb D., Kluge A.G. Parsimony jackknifing outperforms neighbor-joining. Cladistics 1996, 12:99-124.
-
(1996)
Cladistics
, vol.12
, pp. 99-124
-
-
Farris, J.S.1
Albert, V.A.2
Källersjö, M.3
Lipscomb, D.4
Kluge, A.G.5
-
14
-
-
84959792503
-
The number of evolutionary trees
-
Felsenstein J. The number of evolutionary trees. Syst. Zool. 1978, 27:27-33.
-
(1978)
Syst. Zool.
, vol.27
, pp. 27-33
-
-
Felsenstein, J.1
-
15
-
-
84959798530
-
Cases in which parsimony or compatibility methods will be positively misleading
-
Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 1978, 27:401-410.
-
(1978)
Syst. Zool.
, vol.27
, pp. 401-410
-
-
Felsenstein, J.1
-
16
-
-
0000461280
-
Confidence limits on phylogenies: an approach using the bootstrap
-
Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
-
(1985)
Evolution
, vol.39
, pp. 783-791
-
-
Felsenstein, J.1
-
17
-
-
78349298734
-
Branch support via resampling: an empirical study
-
Freudenstein J.V., Davis J.I. Branch support via resampling: an empirical study. Cladistics 2010, 26:643-656.
-
(2010)
Cladistics
, vol.26
, pp. 643-656
-
-
Freudenstein, J.V.1
Davis, J.I.2
-
18
-
-
0028887457
-
Success of maximum likelihood phylogeny inference in the four-taxon case
-
Gaut B.S., Lewis P.O. Success of maximum likelihood phylogeny inference in the four-taxon case. Mol. Biol. Evol. 1995, 12:152-162.
-
(1995)
Mol. Biol. Evol.
, vol.12
, pp. 152-162
-
-
Gaut, B.S.1
Lewis, P.O.2
-
19
-
-
84989455734
-
Character optimization and calculation of tree lengths
-
Goloboff P.A. Character optimization and calculation of tree lengths. Cladistics 1993, 9:433-436.
-
(1993)
Cladistics
, vol.9
, pp. 433-436
-
-
Goloboff, P.A.1
-
20
-
-
0000621757
-
Methods for faster parsimony analysis
-
Goloboff P.A. Methods for faster parsimony analysis. Cladistics 1996, 12:199-220.
-
(1996)
Cladistics
, vol.12
, pp. 199-220
-
-
Goloboff, P.A.1
-
21
-
-
0033499153
-
Analyzing large data sets in reasonable times: solutions for composite optima
-
Goloboff P.A. Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 1999, 15:415-428.
-
(1999)
Cladistics
, vol.15
, pp. 415-428
-
-
Goloboff, P.A.1
-
22
-
-
0035012476
-
Methods for quick consensus estimation
-
Goloboff P.A., Farris J.S. Methods for quick consensus estimation. Cladistics 2001, 17:S26-S34.
-
(2001)
Cladistics
, vol.17
-
-
Goloboff, P.A.1
Farris, J.S.2
-
23
-
-
33644608262
-
Parsimony and Bayesian phylogenetics
-
Oxford University Press, Oxford, V.A. Albert (Ed.)
-
Goloboff P.A., Pol D. Parsimony and Bayesian phylogenetics. Parsimony, Phylogeny, and Genomics 2005, 148-159. Oxford University Press, Oxford. V.A. Albert (Ed.).
-
(2005)
Parsimony, Phylogeny, and Genomics
, pp. 148-159
-
-
Goloboff, P.A.1
Pol, D.2
-
24
-
-
0041738995
-
Improvements to resampling measures of group support
-
Goloboff P.A., Farris J.S., Källersjö M., Oxelman B., Ramírez M.J., Szumik C.A. Improvements to resampling measures of group support. Cladistics 2003, 19:324-332.
-
(2003)
Cladistics
, vol.19
, pp. 324-332
-
-
Goloboff, P.A.1
Farris, J.S.2
Källersjö, M.3
Oxelman, B.4
Ramírez, M.J.5
Szumik, C.A.6
-
25
-
-
45749124657
-
TNT, a free program for phylogenetic analysis
-
Goloboff P.A., Farris J.S., Nixon K.C. TNT, a free program for phylogenetic analysis. Cladistics 2008, 24:774-786.
-
(2008)
Cladistics
, vol.24
, pp. 774-786
-
-
Goloboff, P.A.1
Farris, J.S.2
Nixon, K.C.3
-
26
-
-
66649120526
-
Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups
-
Goloboff P.A., Catalano S.A., Mirande J.M., Szumik C.A., Arias J.S., Källersjö M., Farris J.S. Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups. Cladistics 2009, 25:211-320.
-
(2009)
Cladistics
, vol.25
, pp. 211-320
-
-
Goloboff, P.A.1
Catalano, S.A.2
Mirande, J.M.3
Szumik, C.A.4
Arias, J.S.5
Källersjö, M.6
Farris, J.S.7
-
27
-
-
0020400261
-
New perspectives in the molecular biological analysis of mammalian phylogeny
-
Goodman M., Olson C.B., Beeber J.E., Czelusniak J. New perspectives in the molecular biological analysis of mammalian phylogeny. Acta Zoologica Fennica 1985, 169:19-35.
-
(1985)
Acta Zoologica Fennica
, vol.169
, pp. 19-35
-
-
Goodman, M.1
Olson, C.B.2
Beeber, J.E.3
Czelusniak, J.4
-
28
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
-
Guindon S., Dufayard J.-F., Lefort V., Anisimova M., Hordijk W., Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 2010, 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
-
29
-
-
12044254100
-
The effect of irrelevant characters on bootstrap values
-
Harshman J. The effect of irrelevant characters on bootstrap values. Syst. Biol. 1994, 43:419-424.
-
(1994)
Syst. Biol.
, vol.43
, pp. 419-424
-
-
Harshman, J.1
-
30
-
-
13444259388
-
TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics
-
Jobb G., von Haeseler A., Strimmer K. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol. Biol. 2004, 4:18.
-
(2004)
BMC Evol. Biol.
, vol.4
, pp. 18
-
-
Jobb, G.1
von Haeseler, A.2
Strimmer, K.3
-
31
-
-
0000732090
-
Evolution of protein molecules
-
Academic Press, New York
-
Jukes T.H., Cantor C.R. Evolution of protein molecules. Mammalian Protein Metabolism 1969, vol. 3:21-132. Academic Press, New York.
-
(1969)
Mammalian Protein Metabolism
, vol.3
, pp. 21-132
-
-
Jukes, T.H.1
Cantor, C.R.2
-
32
-
-
0032420129
-
Simultaneous parsimony jackknife analysis of 2538 rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants, and flowering plants
-
Källersjö M., Farris J.S., Chase M.W., Bremer B., Fay M.F., Humphries C.J., Petersen G., Seberg O., Bremer K. Simultaneous parsimony jackknife analysis of 2538 rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants, and flowering plants. Plant Syst. Evol. 1998, 213:259-287.
-
(1998)
Plant Syst. Evol.
, vol.213
, pp. 259-287
-
-
Källersjö, M.1
Farris, J.S.2
Chase, M.W.3
Bremer, B.4
Fay, M.F.5
Humphries, C.J.6
Petersen, G.7
Seberg, O.8
Bremer, K.9
-
33
-
-
45949107473
-
Recent developments in the MAFFT multiple sequence alignment program
-
Katoh K., Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief. Bioinform. 2008, 9:286-298.
-
(2008)
Brief. Bioinform.
, vol.9
, pp. 286-298
-
-
Katoh, K.1
Toh, H.2
-
34
-
-
44149125756
-
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework
-
Katoh K., Toh H. Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. BMC Bioinformatics 2008, 9:212.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 212
-
-
Katoh, K.1
Toh, H.2
-
35
-
-
0037649497
-
Problems due to missing data in phylogenetic analyses including fossils: a critical review
-
Kearney M., Clark J.M. Problems due to missing data in phylogenetic analyses including fossils: a critical review. J. Vertebr. Paleontol. 2003, 23:263-274.
-
(2003)
J. Vertebr. Paleontol.
, vol.23
, pp. 263-274
-
-
Kearney, M.1
Clark, J.M.2
-
36
-
-
0003885805
-
-
Oxford University Press, Oxford, Oxford
-
Kitching I.J., Forey P.L., Humphries C.J., Williams D.M. Cladistics: The Theory and Practice of Parsimony Analysis 1998, Oxford University Press, Oxford, Oxford.
-
(1998)
Cladistics: The Theory and Practice of Parsimony Analysis
-
-
Kitching, I.J.1
Forey, P.L.2
Humphries, C.J.3
Williams, D.M.4
-
37
-
-
84963036271
-
Quantitative phyletics and the evolution of Anurans
-
Kluge A.G., Farris J.S. Quantitative phyletics and the evolution of Anurans. Syst. Zool. 1969, 18:1-32.
-
(1969)
Syst. Zool.
, vol.18
, pp. 1-32
-
-
Kluge, A.G.1
Farris, J.S.2
-
38
-
-
80055110246
-
Estimating phylogenies for species assemblages: a complete phylogeny for the past and present native birds of New Zealand
-
Lanfear R., Bromham L. Estimating phylogenies for species assemblages: a complete phylogeny for the past and present native birds of New Zealand. Mol. Phylogenet. Evol. 2011, 61:958-963.
-
(2011)
Mol. Phylogenet. Evol.
, vol.61
, pp. 958-963
-
-
Lanfear, R.1
Bromham, L.2
-
39
-
-
84865266483
-
Anchored hybrid enrichment for massively high-throughput phylogenomics
-
Lemmon A.R., Emme S.A., Lemmon E.M. Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst. Biol. 2012, 61:727-744.
-
(2012)
Syst. Biol.
, vol.61
, pp. 727-744
-
-
Lemmon, A.R.1
Emme, S.A.2
Lemmon, E.M.3
-
40
-
-
84960569058
-
The discovery and importance of multiple islands of most-parsimonious trees
-
Maddison D.R. The discovery and importance of multiple islands of most-parsimonious trees. Syst. Zool. 1991, 40:315-328.
-
(1991)
Syst. Zool.
, vol.40
, pp. 315-328
-
-
Maddison, D.R.1
-
42
-
-
34547803149
-
Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes
-
McMahon M.M., Sanderson M.J. Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes. Syst. Biol. 2006, 55:818-836.
-
(2006)
Syst. Biol.
, vol.55
, pp. 818-836
-
-
McMahon, M.M.1
Sanderson, M.J.2
-
43
-
-
39549109362
-
Increasing the efficiency of searches for the maximum likelihood tree in a phylogenetic analysis of up to 150 nucleotide sequences
-
Morrison D.A. Increasing the efficiency of searches for the maximum likelihood tree in a phylogenetic analysis of up to 150 nucleotide sequences. Syst. Biol. 2007, 56:988-1010.
-
(2007)
Syst. Biol.
, vol.56
, pp. 988-1010
-
-
Morrison, D.A.1
-
44
-
-
0033504552
-
The parsimony ratchet, a new method for rapid parsimony analysis
-
Nixon K.C. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 1999, 15:407-414.
-
(1999)
Cladistics
, vol.15
, pp. 407-414
-
-
Nixon, K.C.1
-
45
-
-
0002272008
-
Extinction and the origin of species
-
Columbia University Press, New York, Q.D. Wheeler, M. Novacek (Eds.)
-
Nixon K.C., Wheeler Q.D. Extinction and the origin of species. Extinction and Phylogeny 1991, 119-143. Columbia University Press, New York. Q.D. Wheeler, M. Novacek (Eds.).
-
(1991)
Extinction and Phylogeny
, pp. 119-143
-
-
Nixon, K.C.1
Wheeler, Q.D.2
-
46
-
-
80051801316
-
The taming of an impossible child: a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences
-
Peters R.S., Meyer B., Krogmann L., Borner J., Meusemann K., Schutte K., Niehuis O., Misof B. The taming of an impossible child: a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences. BMC Biol. 2011, 9:55.
-
(2011)
BMC Biol.
, vol.9
, pp. 55
-
-
Peters, R.S.1
Meyer, B.2
Krogmann, L.3
Borner, J.4
Meusemann, K.5
Schutte, K.6
Niehuis, O.7
Misof, B.8
-
47
-
-
45849154165
-
JModelTest: phylogenetic model averaging
-
Posada D. JModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 1253-1256
-
-
Posada, D.1
-
48
-
-
80052717965
-
A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians
-
Pyron R.A., Wiens J.J. A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. Mol. Phylogenet. Evol. 2011, 61:543-583.
-
(2011)
Mol. Phylogenet. Evol.
, vol.61
, pp. 543-583
-
-
Pyron, R.A.1
Wiens, J.J.2
-
49
-
-
33645757529
-
Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes
-
Richardson D., Simmons M.P., Reddy A.S.N. Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes. BMC Genomics 2006, 7:18.
-
(2006)
BMC Genomics
, vol.7
, pp. 18
-
-
Richardson, D.1
Simmons, M.P.2
Reddy, A.S.N.3
-
50
-
-
0032030505
-
Phylogenetic supertrees: assembling the trees of life
-
Sanderson M.J., Purvis A., Henze C. Phylogenetic supertrees: assembling the trees of life. Trends Ecol. Evol. 1998, 13:105-109.
-
(1998)
Trends Ecol. Evol.
, vol.13
, pp. 105-109
-
-
Sanderson, M.J.1
Purvis, A.2
Henze, C.3
-
51
-
-
77952490857
-
Phylogenomics with incomplete taxon coverage: the limits of inference
-
Sanderson M.J., McMahon M.J., Steel M. Phylogenomics with incomplete taxon coverage: the limits of inference. BMC Evol. Biol. 2010, 10:155.
-
(2010)
BMC Evol. Biol.
, vol.10
, pp. 155
-
-
Sanderson, M.J.1
McMahon, M.J.2
Steel, M.3
-
52
-
-
0035720643
-
Majority does not rule: the trouble with majority-rule consensus trees
-
Sharkey M.J., Leathers J.W. Majority does not rule: the trouble with majority-rule consensus trees. Cladistics 2001, 17:282-284.
-
(2001)
Cladistics
, vol.17
, pp. 282-284
-
-
Sharkey, M.J.1
Leathers, J.W.2
-
53
-
-
77954501352
-
Unringing a bell: metazoan phylogenomics and the partition bootstrap
-
Siddall M.E. Unringing a bell: metazoan phylogenomics and the partition bootstrap. Cladistics 2010, 26:444-452.
-
(2010)
Cladistics
, vol.26
, pp. 444-452
-
-
Siddall, M.E.1
-
54
-
-
2442507933
-
Independence of alignment and tree search
-
Simmons M.P. Independence of alignment and tree search. Mol. Phylogenet. Evol. 2004, 31:874-879.
-
(2004)
Mol. Phylogenet. Evol.
, vol.31
, pp. 874-879
-
-
Simmons, M.P.1
-
55
-
-
83655167077
-
Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data
-
Simmons M.P. Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data. Mol. Phylogenet. Evol. 2012, 62:472-484.
-
(2012)
Mol. Phylogenet. Evol.
, vol.62
, pp. 472-484
-
-
Simmons, M.P.1
-
56
-
-
84858080561
-
Misleading results of likelihood-based phylogenetic analyses in the presence of missing data
-
Simmons M.P. Misleading results of likelihood-based phylogenetic analyses in the presence of missing data. Cladistics 2012, 28:208-222.
-
(2012)
Cladistics
, vol.28
, pp. 208-222
-
-
Simmons, M.P.1
-
57
-
-
84875054472
-
Quantification and relative severity of inflated branch-support values generated by alternative methods: an empirical example
-
Simmons M.P., Norton A.P. Quantification and relative severity of inflated branch-support values generated by alternative methods: an empirical example. Mol. Phylogenet. Evol. 2013, 67:277-296.
-
(2013)
Mol. Phylogenet. Evol.
, vol.67
, pp. 277-296
-
-
Simmons, M.P.1
Norton, A.P.2
-
58
-
-
0034350427
-
Gaps as characters in sequence-based phylogenetic analyses
-
Simmons M.P., Ochoterena H. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 2000, 49:369-381.
-
(2000)
Syst. Biol.
, vol.49
, pp. 369-381
-
-
Simmons, M.P.1
Ochoterena, H.2
-
59
-
-
33745034045
-
Quantification of the success of phylogenetic inference in simulations
-
Simmons M.P., Webb C.T. Quantification of the success of phylogenetic inference in simulations. Cladistics 2006, 22:249-255.
-
(2006)
Cladistics
, vol.22
, pp. 249-255
-
-
Simmons, M.P.1
Webb, C.T.2
-
60
-
-
0035527375
-
Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses
-
Simmons M.P., Ochoterena H., Carr T.G. Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses. Syst. Biol. 2001, 50:454-462.
-
(2001)
Syst. Biol.
, vol.50
, pp. 454-462
-
-
Simmons, M.P.1
Ochoterena, H.2
Carr, T.G.3
-
61
-
-
78649646272
-
Alignment of, and phylogenetic inference from, random sequences: the susceptibility of alternative alignment methods to creating artifactual resolution and support
-
Simmons M.P., Müller K.F., Norton A.P. Alignment of, and phylogenetic inference from, random sequences: the susceptibility of alternative alignment methods to creating artifactual resolution and support. Mol. Phylogenet. Evol. 2010, 57:1004-1016.
-
(2010)
Mol. Phylogenet. Evol.
, vol.57
, pp. 1004-1016
-
-
Simmons, M.P.1
Müller, K.F.2
Norton, A.P.3
-
62
-
-
84860811512
-
Phylogeny of Celastraceae subfamilies Cassinoideae and Tripterygioideae inferred from morphological characters and nuclear and plastid loci
-
Simmons M.P., Bacon C.D., Cappa J.J., McKenna M.J. Phylogeny of Celastraceae subfamilies Cassinoideae and Tripterygioideae inferred from morphological characters and nuclear and plastid loci. Syst. Bot. 2012, 37:456-467.
-
(2012)
Syst. Bot.
, vol.37
, pp. 456-467
-
-
Simmons, M.P.1
Bacon, C.D.2
Cappa, J.J.3
McKenna, M.J.4
-
63
-
-
83655163776
-
Phylogeny of Celastraceae tribe Euonymeae inferred from morphological characters and nuclear and plastid genes
-
Simmons M.P., McKenna M.J., Bacon C.D., Yakobson K., Cappa J.J., Archer R.H., Ford A.J. Phylogeny of Celastraceae tribe Euonymeae inferred from morphological characters and nuclear and plastid genes. Mol. Phylogenet. Evol. 2012, 62:9-20.
-
(2012)
Mol. Phylogenet. Evol.
, vol.62
, pp. 9-20
-
-
Simmons, M.P.1
McKenna, M.J.2
Bacon, C.D.3
Yakobson, K.4
Cappa, J.J.5
Archer, R.H.6
Ford, A.J.7
-
64
-
-
33750403801
-
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
-
(2006)
Bioinformatics
, vol.22
, pp. 2688-2690
-
-
Stamatakis, A.1
-
65
-
-
84880179914
-
-
The RAxML 7.0.4 manual. (downloaded 16.09.08).
-
Stamatakis, A., 2008. The RAxML 7.0.4 manual. <> (downloaded 16.09.08). http://icwww.epfl.ch/_stamatak/index-Dateien/Page443.htm.
-
(2008)
-
-
Stamatakis, A.1
-
66
-
-
14644397888
-
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
-
Stamatakis A., Ludwig T., Meier H. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 2005, 21:456-463.
-
(2005)
Bioinformatics
, vol.21
, pp. 456-463
-
-
Stamatakis, A.1
Ludwig, T.2
Meier, H.3
-
67
-
-
50249100595
-
A rapid bootstrap algorithm for the RAxML web servers
-
Stamatakis A., Hoover P., Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst. Biol. 2008, 57:758-771.
-
(2008)
Syst. Biol.
, vol.57
, pp. 758-771
-
-
Stamatakis, A.1
Hoover, P.2
Rougemont, J.3
-
68
-
-
77954202497
-
DendroPy: a python library for phylogenetic computing
-
Sukumaran J., Holder M.T. DendroPy: a python library for phylogenetic computing. Bioinformatics 2010, 26:1569-1571.
-
(2010)
Bioinformatics
, vol.26
, pp. 1569-1571
-
-
Sukumaran, J.1
Holder, M.T.2
-
69
-
-
0034918949
-
Global lability, regional resolution, and majority-rule consensus bias
-
Sumrall C.D., Brochu C.A., Merck J.W. Global lability, regional resolution, and majority-rule consensus bias. Paleobiology 2001, 27:254-261.
-
(2001)
Paleobiology
, vol.27
, pp. 254-261
-
-
Sumrall, C.D.1
Brochu, C.A.2
Merck, J.W.3
-
71
-
-
0001336205
-
Phylogenetic inference
-
Sinauer Associates, Inc., Sunderland, D.M. Hillis, C. Moritz, B.K. Mable (Eds.)
-
Swofford D.L., Olsen G.J., Waddell P.J., Hillis D.M. Phylogenetic inference. Molecular Systematics 1996, 407-514. Sinauer Associates, Inc., Sunderland. D.M. Hillis, C. Moritz, B.K. Mable (Eds.).
-
(1996)
Molecular Systematics
, pp. 407-514
-
-
Swofford, D.L.1
Olsen, G.J.2
Waddell, P.J.3
Hillis, D.M.4
-
72
-
-
0141706951
-
The full-length phylogenetic tree from 1551 ribosomal sequences of chitinous fungi
-
Tehler A., Little D.P., Farris J.S. The full-length phylogenetic tree from 1551 ribosomal sequences of chitinous fungi. Mycol. Res. 2003, 107:901-916.
-
(2003)
Mycol. Res.
, vol.107
, pp. 901-916
-
-
Tehler, A.1
Little, D.P.2
Farris, J.S.3
-
73
-
-
77951170797
-
Effects of data incompleteness on the relative performance of parsimony and Bayesian approaches in a supermatrix phylogenetic reconstruction of Mustelidae and Procyonidae (Carnivora)
-
Wolsan M., Sato J.J. Effects of data incompleteness on the relative performance of parsimony and Bayesian approaches in a supermatrix phylogenetic reconstruction of Mustelidae and Procyonidae (Carnivora). Cladistics 2010, 26:168-194.
-
(2010)
Cladistics
, vol.26
, pp. 168-194
-
-
Wolsan, M.1
Sato, J.J.2
-
74
-
-
34547803197
-
PAML 4: phylogenetic analysis by maximum likelihood
-
Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 2007, 24:1586-1591.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
75
-
-
0001336097
-
RbcL sequence data and phylogenetic reconstruction in seed plants: forward
-
Zurawski G., Clegg M.T. RbcL sequence data and phylogenetic reconstruction in seed plants: forward. Ann. Mo. Bot. Gard. 1993, 80:523-525.
-
(1993)
Ann. Mo. Bot. Gard.
, vol.80
, pp. 523-525
-
-
Zurawski, G.1
Clegg, M.T.2
-
76
-
-
33750387249
-
Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets under the Maximum Likelihood Criterion
-
The University of Texas at Austin
-
Zwickl, D.J., 2006. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets under the Maximum Likelihood Criterion. Ph.D. Dissertation, The University of Texas at Austin.
-
(2006)
Ph.D. Dissertation
-
-
Zwickl, D.J.1
-
77
-
-
84880142994
-
-
GARLI 0.96 settings cheat sheet (Smithsonian, June 09). Distributed by the author
-
Zwickl, D.J., 2009. GARLI 0.96 settings cheat sheet (Smithsonian, June 09). Distributed by the author.
-
(2009)
-
-
Zwickl, D.J.1
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