-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul S.F., Madden T.T., Schäffer A.A., Zhang J., Zhang A., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.T.2
Schäffer, A.A.3
Zhang, J.4
Zhang, A.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
4444220955
-
Should we be worried about long-branch attraction in real data sets? : Investigations using metazoan 18S rRNA
-
Anderson F.E., and Swofford D.L. Should we be worried about long-branch attraction in real data sets? : Investigations using metazoan 18S rRNA. Mol. Phyl. Evol. 33 (2004) 440-451
-
(2004)
Mol. Phyl. Evol.
, vol.33
, pp. 440-451
-
-
Anderson, F.E.1
Swofford, D.L.2
-
3
-
-
22944471282
-
Evolutionary sequence analysis of complete eukaryotic genomes
-
Blair J.E., Shah P., and Hedges S.B. Evolutionary sequence analysis of complete eukaryotic genomes. BMC Bioinform. 6 (2005) 53
-
(2005)
BMC Bioinform.
, vol.6
, pp. 53
-
-
Blair, J.E.1
Shah, P.2
Hedges, S.B.3
-
4
-
-
33846491679
-
A phylogenomic study of human, dog, and mouse
-
10.1371/journal.pcbi.0030002
-
Cannarozzi G., Schneider A., and Gonnet G. A phylogenomic study of human, dog, and mouse. PloS Comput. Biol. 3 1 (2007) e2 10.1371/journal.pcbi.0030002
-
(2007)
PloS Comput. Biol.
, vol.3
, Issue.1
-
-
Cannarozzi, G.1
Schneider, A.2
Gonnet, G.3
-
5
-
-
22844440801
-
The systematic component of phylogenetic error as a function of taxonomic sampling under parsimony
-
Debry R.W. The systematic component of phylogenetic error as a function of taxonomic sampling under parsimony. Syst. Biol. 54 (2005) 432-440
-
(2005)
Syst. Biol.
, vol.54
, pp. 432-440
-
-
Debry, R.W.1
-
6
-
-
0025064035
-
The pattern of mammalian evolution and the relative rate of molecular evolution
-
Easteal S. The pattern of mammalian evolution and the relative rate of molecular evolution. Genetics 124 (1990) 165-173
-
(1990)
Genetics
, vol.124
, pp. 165-173
-
-
Easteal, S.1
-
7
-
-
30744460614
-
Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species
-
Fares N.A., Byrne K.P., and Wolfe K.H. Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species. Mol. Biol. Evol. 23 (2006) 245-253
-
(2006)
Mol. Biol. Evol.
, vol.23
, pp. 245-253
-
-
Fares, N.A.1
Byrne, K.P.2
Wolfe, K.H.3
-
8
-
-
84959798530
-
Cases in which parsimony and compatibility methods will be positively misleading
-
Felsenstein J. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27 (1978) 401-410
-
(1978)
Syst. Zool.
, vol.27
, pp. 401-410
-
-
Felsenstein, J.1
-
9
-
-
0000461280
-
Confidence limits on phylogenies: an approach using the bootstrap
-
Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985) 783-791
-
(1985)
Evolution
, vol.39
, pp. 783-791
-
-
Felsenstein, J.1
-
10
-
-
34548525654
-
-
Felsenstein, J., 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5, pp. 164-166.
-
-
-
-
12
-
-
0026911443
-
Higher rates of amino acid substitution in rodents than in humans
-
Gu X., and Li W.-H. Higher rates of amino acid substitution in rodents than in humans. Mol. Phyl. Evol. 1 (1992) 211-214
-
(1992)
Mol. Phyl. Evol.
, vol.1
, pp. 211-214
-
-
Gu, X.1
Li, W.-H.2
-
13
-
-
0000084234
-
A framework for the quantitative study of evolutionary trees
-
Hendy M.D., and Penny D. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38 (1989) 297-309
-
(1989)
Syst. Zool.
, vol.38
, pp. 297-309
-
-
Hendy, M.D.1
Penny, D.2
-
14
-
-
0032023889
-
Taxonomic sampling, phylogenetic accuracy, and investigator bias
-
Hillis D.M. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47 (1998) 3-8
-
(1998)
Syst. Biol.
, vol.47
, pp. 3-8
-
-
Hillis, D.M.1
-
17
-
-
19044362395
-
Gene family content-based phylogeny of prokaryotes: the effect of criteria for inferring homology
-
Hughes A.L., Ekollu V., Friedman R., and Rose J.R. Gene family content-based phylogeny of prokaryotes: the effect of criteria for inferring homology. Syst. Biol. 54 (2005) 268-276
-
(2005)
Syst. Biol.
, vol.54
, pp. 268-276
-
-
Hughes, A.L.1
Ekollu, V.2
Friedman, R.3
Rose, J.R.4
-
18
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones D.T., Taylor W.R., and Thornton J.M. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8 (1992) 275-282
-
(1992)
Comput. Appl. Biosci.
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
19
-
-
13844281341
-
-
Jørgensen, F.G., Hobolth, A., Hornshøj, H., Bendixen, C., Fredholm, M., Schierup, M.H., 2005. Comparative analysis of protein coding sequences from human, mouse, and the domesticated pig. BMC Biology 3, 2. doi:10.1186/1741-7007-3-2.
-
-
-
-
20
-
-
0034992826
-
The closest BLAST hit is often not the nearest neighbor
-
Koski L.B., and Golding G.B. The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol. 52 (2001) 540-542
-
(2001)
J. Mol. Evol.
, vol.52
, pp. 540-542
-
-
Koski, L.B.1
Golding, G.B.2
-
21
-
-
3242810318
-
MEGA3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
-
Kumar S., Tamura K., and Nei M. MEGA3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief. Bioinform. 5 (2004) 150-163
-
(2004)
Brief. Bioinform.
, vol.5
, pp. 150-163
-
-
Kumar, S.1
Tamura, K.2
Nei, M.3
-
22
-
-
0025129816
-
Molecular phylogeny of rodentia, lagomorpha, primates, artiodactyla, and carnivora and molecular clocks
-
Li W.-H., Gouy M., Sharp P.M., O'hUigin C., and Yang Y.-W. Molecular phylogeny of rodentia, lagomorpha, primates, artiodactyla, and carnivora and molecular clocks. Proc. Natl. Acad. Sci. USA 87 (1990) 6703-6707
-
(1990)
Proc. Natl. Acad. Sci. USA
, vol.87
, pp. 6703-6707
-
-
Li, W.-H.1
Gouy, M.2
Sharp, P.M.3
O'hUigin, C.4
Yang, Y.-W.5
-
23
-
-
0141832717
-
Revisting the glires concept - phylogenetic analysis of nuclear sequences
-
Misawa K., and Janke A. Revisting the glires concept - phylogenetic analysis of nuclear sequences. Mol. Phyl. Evol. 28 (2003) 320-327
-
(2003)
Mol. Phyl. Evol.
, vol.28
, pp. 320-327
-
-
Misawa, K.1
Janke, A.2
-
24
-
-
0344243515
-
Reanalysis of Murphy et al.'s data gives various mammalian phylogenies and suggests overcredibility of Bayesian trees
-
Misawa K., and Nei M. Reanalysis of Murphy et al.'s data gives various mammalian phylogenies and suggests overcredibility of Bayesian trees. J. Mol. Evol. 57 (2003) S290-S296
-
(2003)
J. Mol. Evol.
, vol.57
-
-
Misawa, K.1
Nei, M.2
-
25
-
-
0034350422
-
More taxa or more characters revisited: combining data from nuclear protein-encoding genes for phylogenetic analyses of Noctuoidea (Insecta: Lepidoptera)
-
Mitchell A., Mitter C., and Regier G.C. More taxa or more characters revisited: combining data from nuclear protein-encoding genes for phylogenetic analyses of Noctuoidea (Insecta: Lepidoptera). Syst. Biol. 49 (2000) 202-224
-
(2000)
Syst. Biol.
, vol.49
, pp. 202-224
-
-
Mitchell, A.1
Mitter, C.2
Regier, G.C.3
-
26
-
-
0035861441
-
Resolution of the early placental mammal radiation using Bayesian phylogenetics
-
Murphy W.J., Eizirik E., O'Brien S.J., Madsen O., Scally M., Doady C.J., Teeling E., Ryder O.A., Stanhope M.J., de Jong W.W., and Springer M.S. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294 (2001) 2348-2351
-
(2001)
Science
, vol.294
, pp. 2348-2351
-
-
Murphy, W.J.1
Eizirik, E.2
O'Brien, S.J.3
Madsen, O.4
Scally, M.5
Doady, C.J.6
Teeling, E.7
Ryder, O.A.8
Stanhope, M.J.9
de Jong, W.W.10
Springer, M.S.11
-
28
-
-
0032023887
-
Sensitivity of phylogeny estimation to taxonomic sampling
-
Poe S. Sensitivity of phylogeny estimation to taxonomic sampling. Syst. Biol. 47 (1998) 18-31
-
(1998)
Syst. Biol.
, vol.47
, pp. 18-31
-
-
Poe, S.1
-
29
-
-
0035722246
-
Biases in maximum likelihood and parsimony: a simulation approach to a 10-taxon case
-
Pol D., and Siddall M.E. Biases in maximum likelihood and parsimony: a simulation approach to a 10-taxon case. Cladistics 17 (2001) 266-281
-
(2001)
Cladistics
, vol.17
, pp. 266-281
-
-
Pol, D.1
Siddall, M.E.2
-
30
-
-
0036699885
-
Increased taxon sampling is advantageous for phylogenetic inference
-
Pollock D.D., Zwickl D.J., McGuire J.A., and Hillis D.M. Increased taxon sampling is advantageous for phylogenetic inference. Syst. Biol. 51 (2002) 664-671
-
(2002)
Syst. Biol.
, vol.51
, pp. 664-671
-
-
Pollock, D.D.1
Zwickl, D.J.2
McGuire, J.A.3
Hillis, D.M.4
-
32
-
-
0035845536
-
Incomplete taxon sampling is not a problem for phylogenetic inference
-
Rosenberg M.S., and Kumar S. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl. Acad. Sci. USA 58 (2001) 10751-10756
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.58
, pp. 10751-10756
-
-
Rosenberg, M.S.1
Kumar, S.2
-
33
-
-
0037291976
-
Taxon sampling, bioinformatics, and phylogenomics
-
Rosenberg M.S., and Kumar S. Taxon sampling, bioinformatics, and phylogenomics. Syst. Biol. 52 (2003) 119-124
-
(2003)
Syst. Biol.
, vol.52
, pp. 119-124
-
-
Rosenberg, M.S.1
Kumar, S.2
-
34
-
-
0029836454
-
Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies
-
Strimmer K., and von Haeseler A. Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13 (1996) 964-969
-
(1996)
Mol. Biol. Evol.
, vol.13
, pp. 964-969
-
-
Strimmer, K.1
von Haeseler, A.2
-
35
-
-
0031574072
-
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
-
Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 4876-4882
-
-
Thompson, J.D.1
Gibson, T.J.2
Plewniak, F.3
Jeanmougin, F.4
Higgins, D.G.5
-
36
-
-
0029878719
-
Phylogenetic analysis using parsimony and likelihood methods
-
Yang Z. Phylogenetic analysis using parsimony and likelihood methods. J. Mol. Evol. 42 (1996) 294-307
-
(1996)
J. Mol. Evol.
, vol.42
, pp. 294-307
-
-
Yang, Z.1
-
37
-
-
0036699481
-
Increased taxon sampling greatly reduces phylogenetic error
-
Zwickl D.J., and Hillis D.M. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51 (2002) 588-598
-
(2002)
Syst. Biol.
, vol.51
, pp. 588-598
-
-
Zwickl, D.J.1
Hillis, D.M.2
|