-
1
-
-
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
-
2
-
-
0000084234
-
A framework for the quantitative study of evolutionary trees
-
Hendy MD, Penny D: A framework for the quantitative study of evolutionary trees. Syst Zool 1989, 38:297-309.
-
(1989)
Syst Zool
, vol.38
, pp. 297-309
-
-
Hendy, M.D.1
Penny, D.2
-
3
-
-
12044255023
-
Success of phylogenetic methods in the four-taxon case
-
Huelsenbeck JP, Hillis DM: Success of phylogenetic methods in the four-taxon case. Syst Biol 1993, 42:247-264.
-
(1993)
Syst Biol
, vol.42
, pp. 247-264
-
-
Huelsenbeck, J.P.1
Hillis, D.M.2
-
4
-
-
0029113744
-
The robustness of two phylogenetic methods: Four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining
-
Huelsenbeck JP: The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining. Mol Biol Evol 1995, 12:843-849.
-
(1995)
Mol Biol Evol
, vol.12
, pp. 843-849
-
-
Huelsenbeck, J.P.1
-
5
-
-
0034503382
-
Long branch attraction and protist phylogeny
-
Philippe H: Long branch attraction and protist phylogeny. Protist 2000, 51:307-316.
-
(2000)
Protist
, vol.51
, pp. 307-316
-
-
Philippe, H.1
-
6
-
-
0028177080
-
A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
-
Kuhner MK, Felsenstein J: A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol 1994, 11:459-468.
-
(1994)
Mol Biol Evol
, vol.11
, pp. 459-468
-
-
Kuhner, M.K.1
Felsenstein, J.2
-
7
-
-
0028887457
-
Success of maximum likelihood phylogeny inference in the four-taxon case
-
Gaut BS, Lewis PO: 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
-
8
-
-
0035527406
-
Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods
-
Swofford DL, Waddell PJ, Huelsenbeck JP, Foster PG, Lewis PO, Rogers JS: Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst Biol 2001, 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
-
9
-
-
4644252702
-
Tracing the decay of the historical signal in biological sequence data
-
Ho SY, Jermiin L: Tracing the decay of the historical signal in biological sequence data. Syst Biol 2004, 53:623-637.
-
(2004)
Syst Biol
, vol.53
, pp. 623-637
-
-
Ho, S.Y.1
Jermiin, L.2
-
10
-
-
0031084114
-
Is the Felsenstein zone a fly trap?
-
Huelsenbeck JP: Is the Felsenstein zone a fly trap? Syst Biol 1997, 46:69-74.
-
(1997)
Syst Biol
, vol.46
, pp. 69-74
-
-
Huelsenbeck, J.P.1
-
11
-
-
0032148641
-
Systematic bias in phylogenetic analysis: Is the Strepsiptera problem solved?
-
Huelsenbeck JP: Systematic bias in phylogenetic analysis: is the Strepsiptera problem solved? Syst Biol 1998, 47:519-537.
-
(1998)
Syst Biol
, vol.47
, pp. 519-537
-
-
Huelsenbeck, J.P.1
-
12
-
-
4444220955
-
Should we be worried about longbranch attraction in real data sets? Investigations using metazoan 18S rDNA
-
Anderson FE, Swofford DL: Should we be worried about longbranch attraction in real data sets? Investigations using metazoan 18S rDNA. Mol Phylogenet Evol 2004, 33:440-451.
-
(2004)
Mol Phylogenet Evol
, vol.33
, pp. 440-451
-
-
Anderson, F.E.1
Swofford, D.L.2
-
13
-
-
20444491634
-
A review of long-branch attraction
-
Bergsten J: A review of long-branch attraction. Cladistics 2005, 21:163-193.
-
(2005)
Cladistics
, vol.21
, pp. 163-193
-
-
Bergsten, J.1
-
14
-
-
0035339920
-
Molecular phylogenetics: State-ofthe-art methods for looking into the past
-
Whelan S, Lio P, Goldman N: Molecular phylogenetics: state-ofthe-art methods for looking into the past. Trends Genet 2001, 17:262-272.
-
(2001)
Trends Genet
, vol.17
, pp. 262-272
-
-
Whelan, S.1
Lio, P.2
Goldman, N.3
-
15
-
-
0037379673
-
Phylogeny estimation: Traditional and Bayesian approaches
-
Holder M, Lewis PO: Phylogeny estimation: Traditional and Bayesian approaches. Nat Rev Genet 2003, 4:275-284.
-
(2003)
Nat Rev Genet
, vol.4
, pp. 275-284
-
-
Holder, M.1
Lewis, P.O.2
-
17
-
-
0000215283
-
Success of parsimony in the four-taxon case: Longbranch repulsion by likelihood in the Farris zone
-
Siddall ME: Success of parsimony in the four-taxon case: longbranch repulsion by likelihood in the Farris zone. Cladistics 1998, 14:209-220.
-
(1998)
Cladistics
, vol.14
, pp. 209-220
-
-
Siddall, M.E.1
-
18
-
-
0000732090
-
Evolution of protein molecules
-
Edited by: Munro HN. New York, Academic Press
-
Jukes TH, Cantor CR: Evolution of protein molecules. In Mammalian protein metabolism Edited by: Munro HN. New York, Academic Press; 1969:21-132.
-
(1969)
Mammalian Protein Metabolism
, pp. 21-132
-
-
Jukes, T.H.1
Cantor, C.R.2
-
19
-
-
0015219691
-
Fitting discrete probability distributions to evolutionary events
-
Uzzell T, Corbin KW: Fitting discrete probability distributions to evolutionary events. Science 1971, 172:1089-1096.
-
(1971)
Science
, vol.172
, pp. 1089-1096
-
-
Uzzell, T.1
Corbin, K.W.2
-
20
-
-
2442691520
-
A Bayesian mixture model for acrosssite heterogeneities in the amino-acid replacement process
-
Lartillot N, Philippe H: A Bayesian mixture model for acrosssite heterogeneities in the amino-acid replacement process. Mol Biol Evol 2004, 21:1095-1109.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 1095-1109
-
-
Lartillot, N.1
Philippe, H.2
-
21
-
-
4243140058
-
A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data
-
Pagel M, Meade A: A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Syst Biol 2004, 53:571-581.
-
(2004)
Syst Biol
, vol.53
, pp. 571-581
-
-
Pagel, M.1
Meade, A.2
-
22
-
-
0035527373
-
Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated?
-
Sullivan J, Swofford DL: Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated? Syst Biol 2001, 50:723-729.
-
(2001)
Syst Biol
, vol.50
, pp. 723-729
-
-
Sullivan, J.1
Swofford, D.L.2
-
23
-
-
0014860857
-
An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution
-
Fitch WM, Markowitz E: An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem Genet 1970, 4:579-593.
-
(1970)
Biochem Genet
, vol.4
, pp. 579-593
-
-
Fitch, W.M.1
Markowitz, E.2
-
24
-
-
0035399936
-
On the conservation of protein sequences in evolution
-
Philippe H, Lopez P: On the conservation of protein sequences in evolution. Trends in Biochemical Sciences 2001, 26:414-416.
-
(2001)
Trends in Biochemical Sciences
, vol.26
, pp. 414-416
-
-
Philippe, H.1
Lopez, P.2
-
25
-
-
0036134757
-
Heterotachy, an important process of protein evolution
-
Lopez P, Casane D, Philippe H: Heterotachy, an important process of protein evolution. Mol Biol Evol 2002, 19:1-7.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 1-7
-
-
Lopez, P.1
Casane, D.2
Philippe, H.3
-
26
-
-
16344379182
-
Covarion structure in plastid genome evolution: A new statistical test
-
Ane C, Burleigh JG, McMahon MM, Sanderson MJ: Covarion structure in plastid genome evolution: a new statistical test. Mol Biol Evol 2005, 22:914-924.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 914-924
-
-
Ane, C.1
Burleigh, J.G.2
McMahon, M.M.3
Sanderson, M.J.4
-
27
-
-
0029935637
-
Evolution of chlorophyll and bacteriochlorophyll: The problem of invariant sites in sequence analysis
-
Lockhart PJ, Larkum AW, Steel M, Waddell PJ, Penny D: Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis. Proc Natl Acad Sci USA 1996, 93:1930-1934.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 1930-1934
-
-
Lockhart, P.J.1
Larkum, A.W.2
Steel, M.3
Waddell, P.J.4
Penny, D.5
-
28
-
-
0032825223
-
The root of the tree of life in the light of the covarion model
-
Lopez P, Forterre P, Philippe H: The root of the tree of life in the light of the covarion model. J Mol Evol 1999, 49:496-508.
-
(1999)
J Mol Evol
, vol.49
, pp. 496-508
-
-
Lopez, P.1
Forterre, P.2
Philippe, H.3
-
29
-
-
0034019646
-
How molecules evolve in Eubacteria
-
Lockhart PJ, Huson D, Maier U, Fraunholz MJ, Van De Peer Y, Barbrook AC, Howe CJ, Steel MA: How molecules evolve in Eubacteria. Mol Biol Evol 2000, 17:835-838.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 835-838
-
-
Lockhart, P.J.1
Huson, D.2
Maier, U.3
Fraunholz, M.J.4
Van De Peer, Y.5
Barbrook, A.C.6
Howe, C.J.7
Steel, M.A.8
-
30
-
-
0034019771
-
Phylogeny of eukaryotes based on ribosomal RNA: Long-branch attraction and models of sequence evolution
-
Philippe H, Germot A: Phylogeny of eukaryotes based on ribosomal RNA: long-branch attraction and models of sequence evolution. Mol Biol Evol 2000, 17:830-834.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 830-834
-
-
Philippe, H.1
Germot, A.2
-
31
-
-
3042601821
-
Covarion shifts cause a long-branch attraction artifact that unites Microsporidia and Archaebacteria in EF-1{alpha} phylogenies
-
Inagaki Y, Susko E, Fast NM, Roger AJ: Covarion shifts cause a long-branch attraction artifact that unites Microsporidia and Archaebacteria in EF-1{alpha} phylogenies. Mol Biol Evol 2004, 21:1340-1349.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 1340-1349
-
-
Inagaki, Y.1
Susko, E.2
Fast, N.M.3
Roger, A.J.4
-
32
-
-
27744478124
-
Heterotachy and tree building: A case study with plastids and eubacteria
-
Published in Advance Access on September 8, 2005
-
Lockhart PJ, Novis P, Milligan BG, Riden J, Rambaut A, Larkum AW: Heterotachy and tree building: a case study with plastids and eubacteria. Mol Biol Evol 2005, Published in Advance Access on September 8, 2005.:.
-
(2005)
Mol Biol Evol
-
-
Lockhart, P.J.1
Novis, P.2
Milligan, B.G.3
Riden, J.4
Rambaut, A.5
Larkum, A.W.6
-
33
-
-
7244221755
-
Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous
-
Kolaczkowski B, Thornton JW: Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 2004, 431:980-984.
-
(2004)
Nature
, vol.431
, pp. 980-984
-
-
Kolaczkowski, B.1
Thornton, J.W.2
-
34
-
-
26444612274
-
Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous
-
Gadagkar SR, Kumar S: Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous. Mol Biol Evol 2005, 22:2139-2141.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 2139-2141
-
-
Gadagkar, S.R.1
Kumar, S.2
-
35
-
-
17744400517
-
Likelihood, parsimony, and heterogeneous evolution
-
Spencer M, Susko E, Roger AJ: Likelihood, parsimony, and heterogeneous evolution. Mol Biol Evol 2005, 22:1161-1164.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1161-1164
-
-
Spencer, M.1
Susko, E.2
Roger, A.J.3
-
36
-
-
26444556992
-
A call for likelihood phylogenetics even when the process of sequence evolution is heterogeneous
-
in press
-
Gaucher EA, Miyamoto MM: A call for likelihood phylogenetics even when the process of sequence evolution is heterogeneous. Mol Phylogenet Evol 2005, in press:.
-
(2005)
Mol Phylogenet Evol
-
-
Gaucher, E.A.1
Miyamoto, M.M.2
-
37
-
-
27744524191
-
An empirical assessment of long branch attraction artifacts in phylogenomics
-
Brinkmann H, van der Giezen M, Zhou Y, Poncelin de Raucourt G, Philippe H: An empirical assessment of long branch attraction artifacts in phylogenomics. Syst Biol 2005, 54:743-757.
-
(2005)
Syst Biol
, vol.54
, pp. 743-757
-
-
Brinkmann, H.1
Van Der Giezen, M.2
Zhou, Y.3
Poncelin De Raucourt, G.4
Philippe, H.5
-
38
-
-
17744386162
-
Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia
-
Philippe H, Lartillot N, Brinkmann H: Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol Biol Evol 2005, 22:1246-1253.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1246-1253
-
-
Philippe, H.1
Lartillot, N.2
Brinkmann, H.3
-
39
-
-
0036098562
-
Archaeal phylogeny based on ribosomal proteins
-
Matte-Tailliez O, Brochier C, Forterre P, Philippe H: Archaeal phylogeny based on ribosomal proteins. Mol Biol Evol 2002, 19:631-639.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 631-639
-
-
Matte-Tailliez, O.1
Brochier, C.2
Forterre, P.3
Philippe, H.4
-
40
-
-
0036137155
-
Eubacterial phylogeny based on translational apparatus proteins
-
Brochier C, Bapteste E, Moreira D, Philippe H: Eubacterial phylogeny based on translational apparatus proteins. Trends Genet 2002, 18:1-5.
-
(2002)
Trends Genet
, vol.18
, pp. 1-5
-
-
Brochier, C.1
Bapteste, E.2
Moreira, D.3
Philippe, H.4
-
42
-
-
22744445156
-
Monophyly of primary photosynthetic eukaryotes: Green plants, red algae, and glaucophytes
-
Rodriguez-Ezpeleta N, Brinkmann H, Burey SC, Roure B, Burger G, Loffelhardt W, Bohnert HJ, Philippe H, Lang BF: Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes. Curr Biol 2005, 15:1325-1330.
-
(2005)
Curr Biol
, vol.15
, pp. 1325-1330
-
-
Rodriguez-Ezpeleta, N.1
Brinkmann, H.2
Burey, S.C.3
Roure, B.4
Burger, G.5
Loffelhardt, W.6
Bohnert, H.J.7
Philippe, H.8
Lang, B.F.9
-
43
-
-
0015076741
-
The nonidentity of invariable positions in the cytochromes c of different species
-
Fitch WM: The nonidentity of invariable positions in the cytochromes c of different species. Biochem Genet 1971, 5:231-241.
-
(1971)
Biochem Genet
, vol.5
, pp. 231-241
-
-
Fitch, W.M.1
-
44
-
-
0002929101
-
A model of evolutionary change in proteins
-
Edited by: Dayhoff MO. Washington, DC, National Biomedical Research Fundation
-
Dayhoff MO, Eck RV, Park CM: A model of evolutionary change in proteins. In Atlas of protein sequence and structure Volume 5. Edited by: Dayhoff MO. Washington, DC, National Biomedical Research Fundation; 1972:89-99.
-
(1972)
Atlas of Protein Sequence and Structure Volume 5
, vol.5
, pp. 89-99
-
-
Dayhoff, M.O.1
Eck, R.V.2
Park, C.M.3
-
45
-
-
0019296687
-
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
-
Kimura M: A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980, 16:111-120.
-
(1980)
J Mol Evol
, vol.16
, pp. 111-120
-
-
Kimura, M.1
-
46
-
-
0026681831
-
Substitutional bias confounds inference of cyanelle origins from sequence data
-
Lockhart PJ, Howe CJ, Bryant DA, Beanland TJ, Larkum AW: Substitutional bias confounds inference of cyanelle origins from sequence data. J Mol Evol 1992, 34:153-162.
-
(1992)
J Mol Evol
, vol.34
, pp. 153-162
-
-
Lockhart, P.J.1
Howe, C.J.2
Bryant, D.A.3
Beanland, T.J.4
Larkum, A.W.5
-
47
-
-
0003991673
-
-
Sunderland, MA, USA, Sinauer Associates, Inc.
-
Felsenstein J: Inferring phylogenies. Sunderland, MA, USA, Sinauer Associates, Inc.; 2004:645.
-
(2004)
Inferring Phylogenies
, pp. 645
-
-
Felsenstein, J.1
-
48
-
-
0031852105
-
A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages
-
Lockhart PJ, Steel MA, Barbrook AC, Huson D, Charleston MA, Howe CJ: A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages. Mol Biol Evol 1998, 15:1183-1188.
-
(1998)
Mol Biol Evol
, vol.15
, pp. 1183-1188
-
-
Lockhart, P.J.1
Steel, M.A.2
Huson D, B.A.C.3
Charleston, M.A.4
Howe, C.J.5
-
49
-
-
19444384196
-
Should phylogenetic models be trying to 'fit an elephant'?
-
Steel M: Should phylogenetic models be trying to 'fit an elephant'? Trends Genet 2005, 21:307-309.
-
(2005)
Trends Genet
, vol.21
, pp. 307-309
-
-
Steel, M.1
-
50
-
-
19444380847
-
No magic pill for phylogenetic error
-
Thornton JW, Kolaczkowski B: No magic pill for phylogenetic error. Trends Genet 2005, 21:310-311.
-
(2005)
Trends Genet
, vol.21
, pp. 310-311
-
-
Thornton, J.W.1
Kolaczkowski, B.2
-
51
-
-
0030928378
-
Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
-
Rambaut A, Grassly NC: Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci 1997, 13:235-238.
-
(1997)
Comput Appl Biosci
, vol.13
, pp. 235-238
-
-
Rambaut, A.1
Grassly, N.C.2
-
53
-
-
27744503590
-
-
The R Project for Statistical Computing [http://www.rproject. org/]
-
-
-
|