-
2
-
-
0001656793
-
The performance of neighbor-joining methods of phylogenetic reconstruction
-
Atteson, K. 1999. The performance of neighbor-joining methods of phylogenetic reconstruction. Algorithmica 25:251-278.
-
(1999)
Algorithmica
, vol.25
, pp. 251-278
-
-
Atteson, K.1
-
3
-
-
84972528615
-
Bayesian experimental design: A review
-
Chaloner, K., and I. Verdinelli. 1995. Bayesian experimental design: A review. Stat. Sci. 10:273-304.
-
(1995)
Stat. Sci
, vol.10
, pp. 273-304
-
-
Chaloner, K.1
Verdinelli, I.2
-
4
-
-
0034636037
-
Seed plant phylogeny inferred from all three plant genomes: Monophyly of extant gymnosperms and origin of Gnetales from conifers
-
Chaw, S.-M., C. L. Parkinson, Y. Cheng, T. M. Vincent, and J. D. Palmer. 2000. Seed plant phylogeny inferred from all three plant genomes: Monophyly of extant gymnosperms and origin of Gnetales from conifers. Proc. Natl. Acad. Sci. USA 97:4086-1091.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 4086-1091
-
-
Chaw, S.-M.1
Parkinson, C.L.2
Cheng, Y.3
Vincent, T.M.4
Palmer, J.D.5
-
5
-
-
0004128472
-
-
Cambridge University Press, Cambridge, UK
-
Edwards, A. 1972. Likelihood. Cambridge University Press, Cambridge, UK.
-
(1972)
Likelihood
-
-
Edwards, A.1
-
6
-
-
34250305146
-
Identification and analysis of functional elements in 1 % of the human genome by the ENCODE pilot project
-
ENCODE Project Consortium
-
ENCODE Project Consortium. (2007). Identification and analysis of functional elements in 1 % of the human genome by the ENCODE pilot project. Nature 447:799-816.
-
(2007)
Nature
, vol.447
, pp. 799-816
-
-
-
7
-
-
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
-
-
0003991673
-
-
Sinauer Associates, Sunderland, Massachusetts
-
Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates, Sunderland, Massachusetts.
-
(2004)
Inferring phylogenies
-
-
Felsenstein, J.1
-
11
-
-
0028887457
-
Success of maximum likelihood phylogeny inference in the four-taxon case
-
Gaut, B. S., and P. O. Lewis. 1995. Success of maximum likelihood phylogeny inference in the four-taxon case. Mol. Biol. Evol. 12:152-162.
-
(1995)
Mol. Biol. Evol
, vol.12
, pp. 152-162
-
-
Gaut, B.S.1
Lewis, P.O.2
-
12
-
-
33746513101
-
Petaloidy and petal identity MADS-box genes in the balsaminoid genera Impatiens and Marcgravia
-
Geuten, K., A. Becker, K. Kaufmann, P. Caris, S. Janssens, T. Viaene, G. Theissen, and E. Smets. 2006. Petaloidy and petal identity MADS-box genes in the balsaminoid genera Impatiens and Marcgravia. Plant J. 47:501-518.
-
(2006)
Plant J
, vol.47
, pp. 501-518
-
-
Geuten, K.1
Becker, A.2
Kaufmann, K.3
Caris, P.4
Janssens, S.5
Viaene, T.6
Theissen, G.7
Smets, E.8
-
13
-
-
1942453223
-
Conflicting phylogenies of balsaminoid families and the polytomy in Ericales: Combining data in a Bayesian framework
-
Geuten, K., E. Smets, P. Schols, Y.-M. Yuan, S. Janssens, P. Kupfer, and N. Pyck. 2004. Conflicting phylogenies of balsaminoid families and the polytomy in Ericales: Combining data in a Bayesian framework. Mol. Phyl. Evol. 31:711-729.
-
(2004)
Mol. Phyl. Evol
, vol.31
, pp. 711-729
-
-
Geuten, K.1
Smets, E.2
Schols, P.3
Yuan, Y.-M.4
Janssens, S.5
Kupfer, P.6
Pyck, N.7
-
14
-
-
0032558384
-
Phylogenetic information and experimental design in molecular systematics
-
Goldman, N. 1998. Phylogenetic information and experimental design in molecular systematics. Proc. R. Soc. Lond. B 265:1779-1786.
-
(1998)
Proc. R. Soc. Lond. B
, vol.265
, pp. 1779-1786
-
-
Goldman, N.1
-
15
-
-
0041834716
-
Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm
-
Goremykin, V. V., K. I. Hirsch-Ernst, S. Wolfi, and H. F. Hellwig. 2003. Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm. Mol. Biol. Evol. 20:1499-1505.
-
(2003)
Mol. Biol. Evol
, vol.20
, pp. 1499-1505
-
-
Goremykin, V.V.1
Hirsch-Ernst, K.I.2
Wolfi, S.3
Hellwig, H.F.4
-
16
-
-
0032025857
-
Is it better to add taxa or characters to a difficult phylogenetic problem?
-
Graybeal, A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 47:9-17.
-
(1998)
Syst. Biol
, vol.47
, pp. 9-17
-
-
Graybeal, A.1
-
17
-
-
33745120503
-
Seed plant phylogeny: Gnetophytes are derived conifers and a sister group to Pinaceae
-
Hajibabaei, M., J. Xia, and G. Drouin. 2006. Seed plant phylogeny: Gnetophytes are derived conifers and a sister group to Pinaceae. Mol. Phyl. Evol. 40:208-217.
-
(2006)
Mol. Phyl. Evol
, vol.40
, pp. 208-217
-
-
Hajibabaei, M.1
Xia, J.2
Drouin, G.3
-
18
-
-
33747339757
-
Resolution of phylogenetic conflict in large data sets by increased taxon sampling
-
Hedtke, S. M., T. M. Townsend, and D. M. Hillis. 2006. Resolution of phylogenetic conflict in large data sets by increased taxon sampling. Syst. Biol. 55:522-529.
-
(2006)
Syst. Biol
, vol.55
, pp. 522-529
-
-
Hedtke, S.M.1
Townsend, T.M.2
Hillis, D.M.3
-
19
-
-
0000084234
-
A framework for the quantitative study of evolutionary trees
-
Hendy, M. D., and D. Penny. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297-309.
-
(1989)
Syst. Zool
, vol.38
, pp. 297-309
-
-
Hendy, M.D.1
Penny, D.2
-
20
-
-
0242669921
-
Is sparse taxon sampling a problem for phylogenetic inference?
-
Hillis, D. M., D. D. Pollock, J. A. McGuire, and D. J. Zwickl. 2003. Is sparse taxon sampling a problem for phylogenetic inference? Syst. Biol. 52:124-126.
-
(2003)
Syst. Biol
, vol.52
, pp. 124-126
-
-
Hillis, D.M.1
Pollock, D.D.2
McGuire, J.A.3
Zwickl, D.J.4
-
21
-
-
0032746022
-
Disk-Covering, a fast-converging method for phylogenetic tree reconstruction
-
Huson, D. H., S. M. Nettles, and T. J. Warnow. 1999. Disk-Covering, a fast-converging method for phylogenetic tree reconstruction. J. Comput. Biol. 6:369-386.
-
(1999)
J. Comput. Biol
, vol.6
, pp. 369-386
-
-
Huson, D.H.1
Nettles, S.M.2
Warnow, T.J.3
-
22
-
-
0000732090
-
Mammalian protein metabolism
-
H. N. Munro and J. B. Allison, eds, Academic Press, New York
-
Jukes, T. H., and C. R. Cantor. 1969. Mammalian protein metabolism. Pages 21-132 in Evolution of protein molecules (H. N. Munro and J. B. Allison, eds). Academic Press, New York.
-
(1969)
Evolution of protein molecules
, pp. 21-132
-
-
Jukes, T.H.1
Cantor, C.R.2
-
23
-
-
34547401109
-
Optimal experimental design
-
Kiefer, J. 1959. Optimal experimental design. J. Royal Stat. Soc. 21:272319.
-
(1959)
J. Royal Stat. Soc
, vol.21
, pp. 272319
-
-
Kiefer, J.1
-
24
-
-
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
-
25
-
-
0031307210
-
Escaping from the Felsenstein zone by detecting long branches in phylogenetic data
-
Lyons-Weiler, J., and G. A. Hoelzer. 1997. Escaping from the Felsenstein zone by detecting long branches in phylogenetic data. Mol. Phyl. Evol. 8:375-384.
-
(1997)
Mol. Phyl. Evol
, vol.8
, pp. 375-384
-
-
Lyons-Weiler, J.1
Hoelzer, G.A.2
-
26
-
-
18144368560
-
Chloroplast genome phylogenetics: Why we need independent approaches to plant molecular evolution
-
Martin, W., O. Deusch, N. Stawski, N. Grünheit, N., and V. Goremykin. 2005. Chloroplast genome phylogenetics: Why we need independent approaches to plant molecular evolution. Trends Plant Sci. 10:203-209.
-
(2005)
Trends Plant Sci
, vol.10
, pp. 203-209
-
-
Martin, W.O.1
Deusch, N.2
Stawski, N.3
Grünheit, N.4
Goremykin, V.5
-
27
-
-
0034046618
-
EDIBLE: Experimental design and information calculations in phylogenetics
-
Massingham, T., and N. Goldman. 2000. EDIBLE: Experimental design and information calculations in phylogenetics. Bioinformatics 16:294-295.
-
(2000)
Bioinformatics
, vol.16
, pp. 294-295
-
-
Massingham, T.1
Goldman, N.2
-
29
-
-
0032028997
-
Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences
-
Naylor, G. J. P., and W. M. Brown. 1998. Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences. Syst. Biol. 47:61-76.
-
(1998)
Syst. Biol
, vol.47
, pp. 61-76
-
-
Naylor, G.J.P.1
Brown, W.M.2
-
30
-
-
1942453339
-
The sequence of the largest subunit of RNA polymerase II is a useful marker for inferring seed plant phylogeny
-
Nickerson, J., and G. Drouin. 2004. The sequence of the largest subunit of RNA polymerase II is a useful marker for inferring seed plant phylogeny. Mol. Phyl. Evol. 31:403-415.
-
(2004)
Mol. Phyl. Evol
, vol.31
, pp. 403-415
-
-
Nickerson, J.1
Drouin, G.2
-
31
-
-
34547453842
-
Taxon sampling in phylogenetic analysis: Problems and strategies reviewed
-
Department of Systematic Zoology, Uppsala University
-
Nylander, J. A. A. 2001. Taxon sampling in phylogenetic analysis: Problems and strategies reviewed. Introductory research essay no. 1, Department of Systematic Zoology, Uppsala University.
-
(2001)
Introductory research essay
, Issue.1
-
-
Nylander, J.A.A.1
-
33
-
-
27744441025
-
Phylogenomics
-
Philippe, H., F. Delsuc, H. Brinkmann, and N. Lartillot. 2005. Phylogenomics. Annu. Rev. Ecol. Evol. Syst. 36:541-562.
-
(2005)
Annu. Rev. Ecol. Evol. Syst
, vol.36
, pp. 541-562
-
-
Philippe, H.1
Delsuc, F.2
Brinkmann, H.3
Lartillot, N.4
-
34
-
-
3042550872
-
Genome-scale phylogeny and the detection of systematic biases
-
Phillips, M. J., F. Delsuc, and D. Penny. 2004. Genome-scale phylogeny and the detection of systematic biases. Mol. Biol. Evol. 21:1455-1458.
-
(2004)
Mol. Biol. Evol
, vol.21
, pp. 1455-1458
-
-
Phillips, M.J.1
Delsuc, F.2
Penny, D.3
-
35
-
-
0032023887
-
Sensitivity of phylogeny estimation to taxonomic sampling
-
Poe, S. 1998. Sensitivity of phylogeny estimation to taxonomic sampling. Syst. Biol. 47:18-21.
-
(1998)
Syst. Biol
, vol.47
, pp. 18-21
-
-
Poe, S.1
-
36
-
-
0038487279
-
Evaluation of the strategy of long-branch subdivision to improve the accuracy of phylogenetic methods
-
Poe, S. 2003. Evaluation of the strategy of long-branch subdivision to improve the accuracy of phylogenetic methods. Syst. Biol. 52:423-428.
-
(2003)
Syst. Biol
, vol.52
, pp. 423-428
-
-
Poe, S.1
-
37
-
-
0033635920
-
Assessing an unknown evolutionary process: Effect of increasing site-specific knowledge through taxon addition
-
Pollock, D. D., and W. J. Bruno. 2000. Assessing an unknown evolutionary process: Effect of increasing site-specific knowledge through taxon addition. Mol. Biol. Evol. 17:1854-1858.
-
(2000)
Mol. Biol. Evol
, vol.17
, pp. 1854-1858
-
-
Pollock, D.D.1
Bruno, W.J.2
-
38
-
-
0036699885
-
Increased taxon sampling is advantageous for phylogenetic inference
-
Pollock, D. D., D. J. Zwickl, J. A. McGuire, and D. M. Hillis. 2002. Increased taxon sampling is advantageous for phylogenetic inference. Syst. Biol. 51:664-671.
-
(2002)
Syst. Biol
, vol.51
, pp. 664-671
-
-
Pollock, D.D.1
Zwickl, D.J.2
McGuire, J.A.3
Hillis, D.M.4
-
39
-
-
0036855434
-
Improvement of distance-based phylogenetic methods by a local maximum likelihood approach using triplets
-
Ranwez, V., and O. Gascuel. 2002. Improvement of distance-based phylogenetic methods by a local maximum likelihood approach using triplets. Mol. Biol. Evol. 19:1952-1963.
-
(2002)
Mol. Biol. Evol
, vol.19
, pp. 1952-1963
-
-
Ranwez, V.1
Gascuel, O.2
-
41
-
-
0242365676
-
Genome-scale approaches to resolving incongruence in molecular phylogenies
-
Rokas, A., B. Williams, N. King, and S. Carroll. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804.
-
(2003)
Nature
, vol.425
, pp. 798-804
-
-
Rokas, A.1
Williams, B.2
King, N.3
Carroll, S.4
-
42
-
-
0035845536
-
Incomplete taxon sampling is not a problem for phylogenetic inference
-
Rosenberg, M. S., and S. Kumar. 2001. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl Acad. Sci. USA 98:10751-10756.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 10751-10756
-
-
Rosenberg, M.S.1
Kumar, S.2
-
43
-
-
0037291976
-
Taxon sampling, bioinformatics, and phylogenomics
-
Rosenberg, M. S., and S. Kumar. 2003. Taxon sampling, bioinformatics, and phylogenomics. Syst. Biol. 52:119-124.
-
(2003)
Syst. Biol
, vol.52
, pp. 119-124
-
-
Rosenberg, M.S.1
Kumar, S.2
-
44
-
-
0034069504
-
Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants
-
Sanderson, M. J., M. F. Wojciechowski, J. M. Hu, T. S. Khan and S. G. Brady. 2000 Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants. Mol. Biol. Evol. 17:782-797.
-
(2000)
Mol. Biol. Evol
, vol.17
, pp. 782-797
-
-
Sanderson, M.J.1
Wojciechowski, M.F.2
Hu, J.M.3
Khan, T.S.4
Brady, S.G.5
-
45
-
-
0036731325
-
Codon and rate variation models in molecular phylogeny
-
Schadt, E., and K. Lange. 2002. Codon and rate variation models in molecular phylogeny. Mol. Biol. Evol. 19:1534-1549.
-
(2002)
Mol. Biol. Evol
, vol.19
, pp. 1534-1549
-
-
Schadt, E.1
Lange, K.2
-
46
-
-
14744273065
-
Phylogenetics
-
Oxford University Press, Oxford, UK
-
Sempel, C., and M. Steel. 2003. Phylogenetics. Oxford Lecture Series in Mathematics and Its Applications, 24. Oxford University Press, Oxford, UK.
-
(2003)
Oxford Lecture Series in Mathematics and Its Applications
, vol.24
-
-
Sempel, C.1
Steel, M.2
-
47
-
-
4644350604
-
Genome-scale data, angiosperm relationships, and "ending incongruence": A cautionary tale in phylogenetics
-
Soltis, D. E., V. A. Albert, V. Savolainen, K. Hilu, Y. L. Qiu, M. W. Chase, J. S. Farris, S. Stefanovic, D. W. Rice, J. D. Palmer, and P. S. Soltis. 2004. Genome-scale data, angiosperm relationships, and "ending incongruence": A cautionary tale in phylogenetics. Trends Plant Sci. 9:477-483.
-
(2004)
Trends Plant Sci
, vol.9
, pp. 477-483
-
-
Soltis, D.E.1
Albert, V.A.2
Savolainen, V.3
Hilu, K.4
Qiu, Y.L.5
Chase, M.W.6
Farris, J.S.7
Stefanovic, S.8
Rice, D.W.9
Palmer, J.D.10
Soltis, P.S.11
-
48
-
-
34547481992
-
-
Swofford, D. 1998. PAUP*: Phylogenetic analysis using parsimony and other methods, version 4.0 beta. Sinauer Associates, Sunderland, Massachusetts
-
Swofford, D. 1998. PAUP*: Phylogenetic analysis using parsimony (and other methods), version 4.0 beta. Sinauer Associates, Sunderland, Massachusetts.
-
-
-
-
49
-
-
0035527406
-
Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods
-
Swofford, D. L., P. J. Waddell, J. P. Huelsenbeck, P. G. Foster, P. O. Lewis, and J. S. Rogers. 2001. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 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
-
50
-
-
3342920601
-
Prospects for inferring very large phylogenies by using the neighbor-joining method
-
Tamura, K., M. Nei, and S. Kumar. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc. Natl Acad. Sci. USA 101:11030-11035.
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 11030-11035
-
-
Tamura, K.1
Nei, M.2
Kumar, S.3
-
51
-
-
0004062749
-
-
5th Edition. Addison-Wesley, Reading, Massachusetts
-
Wolfram, S. 2003. Mathematica, 5th Edition. Addison-Wesley, Reading, Massachusetts.
-
(2003)
Mathematica
-
-
Wolfram, S.1
-
52
-
-
0029878719
-
Phylogenetic analysis using parsimony and likelihood methods
-
Yang, Z. 1996a. Phylogenetic analysis using parsimony and likelihood methods. J. Mol. Evol. 42:294-307.
-
(1996)
J. Mol. Evol
, vol.42
, pp. 294-307
-
-
Yang, Z.1
-
53
-
-
0029970097
-
Maximum-likelihood models for combined analyses of multiple sequence data
-
Yang, Z. 1996b. Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42:587-596.
-
(1996)
J. Mol. Evol
, vol.42
, pp. 587-596
-
-
Yang, Z.1
-
54
-
-
0030683599
-
PAML: A program package for phylogenetic analysis by maximum likelihood
-
Yang, Z. 1997. PAML: A program package for phylogenetic analysis by maximum likelihood. CABIOS 13:555-556.
-
(1997)
CABIOS
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
55
-
-
0029469716
-
Maximum likelihood trees from DNA sequences: A peculiar statistical estimation problem
-
Yang, Z., N. Goldman, and A. Friday. 1995. Maximum likelihood trees from DNA sequences: A peculiar statistical estimation problem. Syst. Biol. 44:384-399.
-
(1995)
Syst. Biol
, vol.44
, pp. 384-399
-
-
Yang, Z.1
Goldman, N.2
Friday, A.3
-
56
-
-
0002275128
-
Constructing trees from the set of distances be-tween pendant vertices
-
Nauk, in Russian
-
Zaretskii, K. A. 1965. Constructing trees from the set of distances be-tween pendant vertices. Uspehi Mathematiceskih Nauk 20:90-92 (in Russian).
-
(1965)
Uspehi Mathematiceskih
, vol.20
, pp. 90-92
-
-
Zaretskii, K.A.1
-
57
-
-
0036699481
-
Increased taxon sampling greatly reduces phylogenetic error
-
Zwickl, D. J., and D. M. Hillis. 2002. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51:588-598.
-
(2002)
Syst. Biol
, vol.51
, pp. 588-598
-
-
Zwickl, D.J.1
Hillis, D.M.2
|