-
1
-
-
16344379182
-
Covarion structure in plastid genome evolution: A new statistical test
-
Ané C, Burleigh JG, McMahon MM, Sanderson MJ. 2005. Covarion structure in plastid genome evolution: a new statistical test. Mol Biol Evol. 22:914-924.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 914-924
-
-
Ané, C.1
Burleigh, J.G.2
McMahon, M.M.3
Sanderson, M.J.4
-
2
-
-
0034602344
-
A kingdom-level phylogeny of eukaryotes based on combined protein data
-
Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF. 2000. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972-977.
-
(2000)
Science
, vol.290
, pp. 972-977
-
-
Baldauf, S.L.1
Roger, A.J.2
Wenk-Siefert, I.3
Doolittle, W.F.4
-
4
-
-
17744394753
-
Phylogenomics and the reconstruction of the tree of life
-
Delsuc F, Brinkmann H, Philippe H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 6: 361-375.
-
(2005)
Nat Rev Genet
, vol.6
, pp. 361-375
-
-
Delsuc, F.1
Brinkmann, H.2
Philippe, H.3
-
5
-
-
42149157760
-
Broad phylogenomic sampling improves resolution of the animal tree of life
-
(18 co-authors)
-
Dunn CW, Hejnol A, Matus DQ, et al. (18 co-authors). 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749.
-
(2008)
Nature
, vol.452
, pp. 745-749
-
-
Dunn, C.W.1
Hejnol, A.2
Matus, D.Q.3
-
6
-
-
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
-
8
-
-
0035029534
-
Maximum-likelihood phylogenetic analysis under a covarion-like model
-
Galtier N. 2001. Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol Biol Evol. 18:866-873.
-
(2001)
Mol Biol Evol
, vol.18
, pp. 866-873
-
-
Galtier, N.1
-
9
-
-
0035895207
-
Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors
-
Gaucher EA, Miyamoto MM, Benner SA. 2001. Function-structure analysis of proteins using covarion-based evolutionary approaches: elongation factors. Proc Natl Acad Sci USA. 98: 548-552.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 548-552
-
-
Gaucher, E.A.1
Miyamoto, M.M.2
Benner, S.A.3
-
10
-
-
45849119373
-
Difficulties in testing for covarion-like properties of sequences under the confounding influence of changing proportions of variable sites
-
Gruenheit N, Lockhart PJ, Steel M, Martin W. 2008. Difficulties in testing for covarion-like properties of sequences under the confounding influence of changing proportions of variable sites. Mol Biol Evol. 25:1512-1520.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 1512-1520
-
-
Gruenheit, N.1
Lockhart, P.J.2
Steel, M.3
Martin, W.4
-
11
-
-
0036097894
-
Testing a covariotide model of DNA substitution
-
Huelsenbeck JP. 2002. Testing a covariotide model of DNA substitution. Mol Biol Evol. 19:698-707.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 698-707
-
-
Huelsenbeck, J.P.1
-
12
-
-
38649092410
-
Dendroscope: An interactive viewer for large phylogenetic trees
-
Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R. 2007. Dendroscope: an interactive viewer for large phylogenetic trees. BMC Bioinformatics. 8:460.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 460
-
-
Huson, D.H.1
Richter, D.C.2
Rausch, C.3
Dezulian, T.4
Franz, M.5
Rupp, R.6
-
13
-
-
65349193401
-
Gene sampling can bias multi-gene phylogenetic inferences: The relationship between red algae and green plants as a case study
-
Inagaki Y, Nakajima Y, Sato M, Sakaguchi M, Hashimoto T. 2009. Gene sampling can bias multi-gene phylogenetic inferences: the relationship between red algae and green plants as a case study. Mol Biol Evol. 26:1171-1178.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 1171-1178
-
-
Inagaki, Y.1
Nakajima, Y.2
Sato, M.3
Sakaguchi, M.4
Hashimoto, T.5
-
14
-
-
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. 2004. Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1 alpha phylogenies. Mol Biol Evol. 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
-
15
-
-
7244221755
-
Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous
-
Kolaczkowski B, Thornton JW. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980-984.
-
(2004)
Nature
, vol.431
, pp. 980-984
-
-
Kolaczkowski, B.1
Thornton, J.W.2
-
16
-
-
44649184070
-
A mixed branch length model of heterotachy improves phylogenetic accuracy
-
Kolaczkowski B, Thornton JW. 2008. A mixed branch length model of heterotachy improves phylogenetic accuracy. Mol Biol Evol. 25:1054-1066.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 1054-1066
-
-
Kolaczkowski, B.1
Thornton, J.W.2
-
17
-
-
28944440718
-
Heterotachy and tree building: A case study with plastids and eubacteria
-
Lockhart P, Novis P, Milligan BG, Riden J, Rambaut A, Larkum T. 2006. Heterotachy and tree building: a case study with plastids and eubacteria. Mol Biol Evol. 23:40-45.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 40-45
-
-
Lockhart, P.1
Novis, P.2
Milligan, B.G.3
Riden, J.4
Rambaut, A.5
Larkum, T.6
-
18
-
-
26444605036
-
A tale of two processes
-
Lockhart P, Steel M. 2005. A tale of two processes. Syst Biol. 54:948-951.
-
(2005)
Syst Biol
, vol.54
, pp. 948-951
-
-
Lockhart, P.1
Steel, M.2
-
19
-
-
0036134757
-
Heterotachy, an important process of protein evolution
-
Lopez P, Casane D, Philippe H. 2002. Heterotachy, an important process of protein evolution. Mol Biol Evol. 19:1-7.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 1-7
-
-
Lopez, P.1
Casane, D.2
Philippe, H.3
-
20
-
-
0032516147
-
Gene transfer to the nucleus and the evolution of chloroplasts
-
Martin W, Stoebe B, Goremykin V, Hansmann S, Hasegawa M, Kowallik KV. 1998. Gene transfer to the nucleus and the evolution of chloroplasts. Nature 393:162-165.
-
(1998)
Nature
, vol.393
, pp. 162-165
-
-
Martin, W.1
Stoebe, B.2
Goremykin, V.3
Hansmann, S.4
Hasegawa, M.5
Kowallik, K.V.6
-
21
-
-
38449104891
-
Phylogenetic mixtures on a single tree can mimic a tree of another topology
-
Matsen FA, Steel M. 2007. Phylogenetic mixtures on a single tree can mimic a tree of another topology. Syst Biol. 56:767-775.
-
(2007)
Syst Biol
, vol.56
, pp. 767-775
-
-
Matsen, F.A.1
Steel, M.2
-
22
-
-
0037815065
-
Heterotachy and functional shift in protein evolution
-
Philippe H, Casane D, Gribaldo S, Lopez P, Meunier J. 2003. Heterotachy and functional shift in protein evolution. IUBMB Life. 55:257-265.
-
(2003)
IUBMB Life
, vol.55
, pp. 257-265
-
-
Philippe, H.1
Casane, D.2
Gribaldo, S.3
Lopez, P.4
Meunier, J.5
-
23
-
-
0034019771
-
Phylogeny of eukaryotes based on ribosomal RNA: Long-branch attraction and models of sequence evolution
-
Philippe H, Germot A. 2000. Phylogeny of eukaryotes based on ribosomal RNA: long-branch attraction and models of sequence evolution. Mol Biol Evol. 17:830-834.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 830-834
-
-
Philippe, H.1
Germot, A.2
-
24
-
-
27744488568
-
Heterotachy and long-branch attraction in phylogenetics
-
Philippe H, Zhou Y, Brinkmann H, Rodrigue N, Delsuc F. 2005. Heterotachy and long-branch attraction in phylogenetics. BMC Evol Biol. 5:50.
-
(2005)
BMC Evol Biol
, vol.5
, pp. 50
-
-
Philippe, H.1
Zhou, Y.2
Brinkmann, H.3
Rodrigue, N.4
Delsuc, F.5
-
26
-
-
0031284363
-
On the consistency of maximum likelihood estimation of phylogenetic trees from nucleotide sequences
-
Rogers JS. 1997. On the consistency of maximum likelihood estimation of phylogenetic trees from nucleotide sequences. Syst Biol. 46:354-357.
-
(1997)
Syst Biol
, vol.46
, pp. 354-357
-
-
Rogers, J.S.1
-
27
-
-
58149293644
-
LineageSpecificSeqgen: Generating sequence data with lineage-specific variation in the proportion of variable sites
-
[Erratum in BMC Evol Biol 9, 2009]
-
Shavit Grievink L, Penny D, Hendy MD, Holland BR. 2008. LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites. BMC Evol Biol. 8:317.[Erratum in BMC Evol Biol 9, 2009].
-
(2008)
BMC Evol Biol
, vol.8
, pp. 317
-
-
Shavit Grievink, L.1
Penny, D.2
Hendy, M.D.3
Holland, B.R.4
-
28
-
-
0029844787
-
Large differences in substitutional pattern and evolutionary rate of 12S ribosomal RNA genes
-
Simon C, Nigro L, Sullivan J, Holsinger K, Martin A, Grapputo A, Franke A, McIntosh C. 1996. Large differences in substitutional pattern and evolutionary rate of 12S ribosomal RNA genes. Mol Biol Evol. 13:923-932.
-
(1996)
Mol Biol Evol
, vol.13
, pp. 923-932
-
-
Simon, C.1
Nigro, L.2
Sullivan, J.3
Holsinger, K.4
Martin, A.5
Grapputo, A.6
Franke, A.7
McIntosh, C.8
-
29
-
-
33646929523
-
Harvesting the fruit of the human mtDNA tree
-
Torroni A, Achilli A, Macaulay V, Richards M, Bandelt HJ. 2006. Harvesting the fruit of the human mtDNA tree. Trends Genet. 22:339-345.
-
(2006)
Trends Genet
, vol.22
, pp. 339-345
-
-
Torroni, A.1
Achilli, A.2
MacAulay, V.3
Richards, M.4
Bandelt, H.J.5
-
30
-
-
0031986279
-
Modeling the covarion hypothesis of nucleotide substitution
-
Tuffley C, Steel M. 1998. Modeling the covarion hypothesis of nucleotide substitution. Math Biosci. 147:63-91.
-
(1998)
Math Biosci
, vol.147
, pp. 63-91
-
-
Tuffley, C.1
Steel, M.2
-
31
-
-
33845900956
-
Testing for covarion-like evolution in protein sequences
-
Wang HC, Spencer M, Susko E, Roger AJ. 2007. Testing for covarion-like evolution in protein sequences. Mol Biol Evol. 24:294-305.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 294-305
-
-
Wang, H.C.1
Spencer, M.2
Susko, E.3
Roger, A.J.4
-
32
-
-
34548633617
-
New approaches to phylogenetic tree search and their application to large numbers of protein alignments
-
Whelan S. 2007. New approaches to phylogenetic tree search and their application to large numbers of protein alignments. Syst Biol. 56:727-740.
-
(2007)
Syst Biol
, vol.56
, pp. 727-740
-
-
Whelan, S.1
-
34
-
-
47649095950
-
Spatial and temporal heterogeneity in nucleotide sequence evolution
-
Whelan S. 2008b. Spatial and temporal heterogeneity in nucleotide sequence evolution. Mol Biol Evol. 25:1683-1694.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 1683-1694
-
-
Whelan, S.1
-
35
-
-
57149108257
-
The genetic code can cause systematic bias in simple phylogenetic models
-
Whelan S. 2008c. The genetic code can cause systematic bias in simple phylogenetic models. Philos Trans R Soc Lond B Biol Sci. 363:4003-4011.
-
(2008)
Philos Trans R Soc Lond B Biol Sci
, vol.363
, pp. 4003-4011
-
-
Whelan, S.1
-
36
-
-
0035031966
-
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
-
Whelan S, Goldman N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol. 18:691-699.
-
(2001)
Mol Biol Evol
, vol.18
, pp. 691-699
-
-
Whelan, S.1
Goldman, N.2
-
37
-
-
0028064845
-
Maximum-likelihood phylogenetic estimation from DNA-sequences with variable rates over sites-approximate methods
-
Yang ZH. 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
-
-
Zh, Y.1
|