-
1
-
-
0034043778
-
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
-
Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17:540-552.
-
(2000)
Mol Biol Evol.
, vol.17
, pp. 540-552
-
-
Castresana, J.1
-
2
-
-
37849023306
-
Assessing performance of orthology detection strategies applied to eukaryotic genomes
-
Chen F, Mackey AJ, Vermunt JK, Roos DS. 2007. Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS ONE. 2:e383.
-
(2007)
PLoS ONE.
, vol.2
-
-
Chen, F.1
MacKey, A.J.2
Vermunt, J.K.3
Roos, D.S.4
-
3
-
-
0141721403
-
Indels in protein-coding sequences of Euarchontoglires constrain the rooting of the eutherian tree
-
de Jong WW, van Dijk MA, Poux C, Kappe G, van Rheede T, Madsen O. 2003. Indels in protein-coding sequences of Euarchontoglires constrain the rooting of the eutherian tree. Mol Phylogenet Evol. 28:328-340.
-
(2003)
Mol Phylogenet Evol
, vol.28
, pp. 328-340
-
-
De Jong, W.W.1
Van Dijk, M.A.2
Poux, C.3
Kappe, G.4
Van Rheede, T.5
Madsen, O.6
-
4
-
-
33745021824
-
Mitochondrial genome of Trichoplax adhaerens supports Placozoa as the basal lower metazoan phylum
-
Dellaporta SL, Xu A, Sagasser S, Jakob W, Moreno MA, Buss LW, Schierwater B. 2006. Mitochondrial genome of Trichoplax adhaerens supports Placozoa as the basal lower metazoan phylum. Proc Natl Acad Sci USA. 103:8751-8756.
-
(2006)
Proc Natl Acad Sci USA.
, vol.103
, pp. 8751-8756
-
-
Dellaporta, S.L.1
Xu, A.2
Sagasser, S.3
Jakob, W.4
Moreno, M.A.5
Buss, L.W.6
Schierwater, B.7
-
5
-
-
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
-
6
-
-
0033178886
-
Intron-exon structures of eukaryotic model organisms
-
Deutsch M, Long M. 1999. Intron-exon structures of eukaryotic model organisms. Nucleic Acids Res. 27:3219-3228.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 3219-3228
-
-
Deutsch, M.1
Long, M.2
-
7
-
-
14644430471
-
ProbCons: Probabilistic consistency-based multiple sequence alignment
-
Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. 2005. ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res. 15:330-340.
-
(2005)
Genome Res.
, vol.15
, pp. 330-340
-
-
Do, C.B.1
Mahabhashyam, M.S.2
Brudno, M.3
Batzoglou, S.4
-
8
-
-
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
-
9
-
-
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
-
10
-
-
0000461280
-
Confidence-limits on phylogenies\-an approach using the bootstrap
-
Felsenstein J. 1985. Confidence-limits on phylogenies\-an approach using the bootstrap. Evolution 39:783-791.
-
(1985)
Evolution
, vol.39
, pp. 783-791
-
-
Felsenstein, J.1
-
12
-
-
4544296370
-
Bayesian inference of the metazoan phylogeny: A combined molecular and morphological approach
-
Glenner H, Hansen AJ, Sorensen MV, Ronquist F, Huelsenbeck JP, Willerslev E. 2004. Bayesian inference of the metazoan phylogeny: a combined molecular and morphological approach. Curr Biol. 14:1644-1649.
-
(2004)
Curr Biol
, vol.14
, pp. 1644-1649
-
-
Glenner, H.1
Hansen, A.J.2
Sorensen, M.V.3
Ronquist, F.4
Huelsenbeck, J.P.5
Willerslev, E.6
-
13
-
-
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
-
14
-
-
0035756272
-
The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins
-
Gupta RS. 2001. The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins. Int Microbiol. 4:187-202.
-
(2001)
Int Microbiol.
, vol.4
, pp. 187-202
-
-
Gupta, R.S.1
-
15
-
-
33748176992
-
Molecular signatures (unique proteins and conserved indels) that are specific for the epsilon proteobacteria (Campylobacterales)
-
Gupta RS. 2006. Molecular signatures (unique proteins and conserved indels) that are specific for the epsilon proteobacteria (Campylobacterales). BMC Genomics. 7:167.
-
(2006)
BMC Genomics.
, vol.7
, Issue.167
-
-
Gupta, R.S.1
-
16
-
-
39049145171
-
Phylogenomics and signature proteins for the alpha proteobacteria and its main groups
-
Gupta RS, Mok A. 2007. Phylogenomics and signature proteins for the alpha proteobacteria and its main groups. BMC Microbiol. 7:106.
-
(2007)
BMC Microbiol
, vol.7
, pp. 106
-
-
Gupta, R.S.1
Mok, A.2
-
17
-
-
34547697011
-
Glass sponges and bilaterian animals share derived mitochondrial genomic features: A common ancestry or parallel evolution?
-
Haen KM, Lang BF, Pomponi SA, Lavrov DV. 2007. Glass sponges and bilaterian animals share derived mitochondrial genomic features: a common ancestry or parallel evolution? Mol Biol Evol. 24:1518-1527.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1518-1527
-
-
Haen, K.M.1
Lang, B.F.2
Pomponi, S.A.3
Lavrov, D.V.4
-
18
-
-
3242690862
-
The new view of animal phylogeny
-
Halanych KM. 2004. The new view of animal phylogeny. Annu Rev Ecol Evol Syst. 35:229-256.
-
(2004)
Annu Rev Ecol Evol Syst.
, vol.35
, pp. 229-256
-
-
Halanych, K.M.1
-
19
-
-
33749653678
-
A new species of Amphimedon (Porifera, Demospongiae, Haplosclerida, Niphatidae) from the Capricorn-Bunker Group of Islands, Great Barrier Reef, Australia: Target species for the 'sponge genome project'
-
Hooper JNA, Van Soest RWM. 2006. A new species of Amphimedon (Porifera, Demospongiae, Haplosclerida, Niphatidae) from the Capricorn-Bunker Group of Islands, Great Barrier Reef, Australia: target species for the 'sponge genome project'. Zootaxa. 1314:31-39.
-
(2006)
Zootaxa.
, vol.1314
, pp. 31-39
-
-
Hooper, J.N.A.1
Van Soest, R.W.M.2
-
20
-
-
0032849859
-
CAP3: A DNA sequence assembly program
-
Huang X, Madan A. 1999. CAP3: a DNA sequence assembly program. Genome Res. 9:868-877.
-
(1999)
Genome Res.
, vol.9
, pp. 868-877
-
-
Huang, X.1
Madan, A.2
-
21
-
-
34547755564
-
Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata
-
Irimia M, Maeso I, Penny D, Garcia-Fernandez J, Roy SW. 2007. Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata. Mol Biol Evol. 24:1604-1607.
-
(2007)
Mol Biol Evol.
, vol.24
, pp. 1604-1607
-
-
Irimia, M.1
Maeso, I.2
Penny, D.3
Garcia-Fernandez, J.4
Roy, S.W.5
-
22
-
-
0033290515
-
ESTScan: A program for detecting, evaluating, and reconstructing potential coding regions in EST sequences
-
Iseli C, Jongeneel CV, Bucher P. 1999. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol. 138-148.
-
(1999)
Proc Int Conf Intell Syst Mol Biol.
, pp. 138-148
-
-
Iseli, C.1
Jongeneel, C.V.2
Bucher, P.3
-
23
-
-
39149110563
-
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans
-
36 co-authors
-
King N, Westbrook MJ, Young SL, et al. (36 co-authors). 2008. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 451:783-788.
-
(2008)
Nature
, vol.451
, pp. 783-788
-
-
King, N.1
Westbrook, M.J.2
Young, S.L.3
-
24
-
-
34548088457
-
Heads or tails: A simple reliability check for multiple sequence alignments
-
Landan G, Graur D. 2007. Heads or tails: a simple reliability check for multiple sequence alignments. Mol Biol Evol. 24:1380-1383.
-
(2007)
Mol Biol Evol.
, vol.24
, pp. 1380-1383
-
-
Landan, G.1
Graur, D.2
-
25
-
-
0028696608
-
The comparison of morphological and molecular data in phylogenetic systematics
-
Larson A. 1994. The comparison of morphological and molecular data in phylogenetic systematics. Exs. 69:371-390.
-
(1994)
Exs.
, vol.69
, pp. 371-390
-
-
Larson, A.1
-
26
-
-
34248159030
-
Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model
-
Lartillot N, Brinkmann H, Philippe H. 2007. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol. 7(Suppl 1):S4.
-
(2007)
BMC Evol Biol.
, vol.7
, Issue.SUPPL. 1
-
-
Lartillot, N.1
Brinkmann, H.2
Philippe, H.3
-
27
-
-
40549115956
-
Improvement of molecular phyloge-netic inference and the phylogeny of Bilateria
-
Lartillot N, Philippe H. 2008. Improvement of molecular phyloge-netic inference and the phylogeny of Bilateria. Philos Trans R Soc Lond B Biol Sci. 363:1463-1472.
-
(2008)
Philos Trans R Soc Lond B Biol Sci
, vol.363
, pp. 1463-1472
-
-
Lartillot, N.1
Philippe, H.2
-
29
-
-
84993911710
-
Multi-residue gaps, a class of molecular characters with exceptional reliability for phylogenetic analyses
-
Lloyd DG, Calder VL. 1991. Multi-residue gaps, a class of molecular characters with exceptional reliability for phylogenetic analyses. J Evol Biol. 4:9-21.
-
(1991)
J Evol Biol.
, vol.4
, pp. 9-21
-
-
Lloyd, D.G.1
Calder, V.L.2
-
30
-
-
0035859814
-
Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA
-
Medina M, Collins AG, Silberman JD, Sogin ML. 2001. Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA. Proc Natl Acad Sci USA. 98:9707-9712.
-
(2001)
Proc Natl Acad Sci USA.
, vol.98
, pp. 9707-9712
-
-
Medina, M.1
Collins, A.G.2
Silberman, J.D.3
Sogin, M.L.4
-
31
-
-
33244488048
-
Incorporating information from length-mutational events into phylogenetic analysis
-
Müller K. 2006. Incorporating information from length-mutational events into phylogenetic analysis. Mol Phylogenet Evol. 38: 667-676.
-
(2006)
Mol Phylogenet Evol.
, vol.38
, pp. 667-676
-
-
Müller, K.1
-
32
-
-
22944482184
-
SeqState: Primer design and sequence statistics for phylogenetic DNA datasets
-
Müller K. 2005. SeqState: primer design and sequence statistics for phylogenetic DNA datasets. Appl Bioinformatics. 4:65-69.
-
(2005)
Appl Bioinformatics.
, vol.4
, pp. 65-69
-
-
Müller, K.1
-
33
-
-
17744379783
-
The Opisthokonta and the Ecdysozoa may not be clades: Stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Ecdysozoa
-
Philip GK, Creevey CJ, McInerney JO. 2005. The Opisthokonta and the Ecdysozoa may not be clades: stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Ecdysozoa. Mol Biol Evol. 22:1175-1184.
-
(2005)
Mol Biol Evol.
, vol.22
, pp. 1175-1184
-
-
Philip, G.K.1
Creevey, C.J.2
McInerney, J.O.3
-
34
-
-
65249099546
-
Phylogenomics revives traditional views on deep animal relationships
-
21 co-authors
-
Philippe H, Derelle R, Lopez P, et al. (21 co-authors). 2009. Phylogenomics revives traditional views on deep animal relationships. Curr Biol. 19:706-712.
-
(2009)
Curr Biol.
, vol.19
, pp. 706-712
-
-
Philippe, H.1
Derelle, R.2
Lopez, P.3
-
35
-
-
17744386162
-
Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia
-
Philippe H, Lartillot N, Brinkmann H. 2005. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol Biol Evol. 22:1246-1253.
-
(2005)
Mol Biol Evol.
, vol.22
, pp. 1246-1253
-
-
Philippe, H.1
Lartillot, N.2
Brinkmann, H.3
-
37
-
-
33846057724
-
NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
-
Pruitt KD, Tatusova T, Maglott DR. 2007. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35: D61-D65.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Pruitt, K.D.1
Tatusova, T.2
Maglott, D.R.3
-
39
-
-
37549040975
-
Analysis of rare amino acid replacements supports the coelomata clade
-
Rogozin IB, Wolf YI, Carmel L, Koonin EV. 2007a. Analysis of rare amino acid replacements supports the coelomata clade. Mol Biol Evol. 24:2594-2597.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 2594-2597
-
-
Rogozin, I.B.1
Wolf, Y.I.2
Carmel, L.3
Koonin, E.V.4
-
40
-
-
34047227628
-
Ecdysozoan clade rejected by genome-wide analysis of rare amino acid replacements
-
Rogozin IB, Wolf YI, Carmel L, Koonin EV. 2007b. Ecdysozoan clade rejected by genome-wide analysis of rare amino acid replacements. Mol Biol Evol. 24:1080-1090.
-
(2007)
Mol Biol Evol.
, vol.24
, pp. 1080-1090
-
-
Rogozin, I.B.1
Wolf, Y.I.2
Carmel, L.3
Koonin, E.V.4
-
41
-
-
0033793019
-
Rare genomic changes as a tool for phylogenetics
-
Rokas A, Holland PW. 2000. Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol. 15:454-459.
-
(2000)
Trends Ecol Evol.
, vol.15
, pp. 454-459
-
-
Rokas, A.1
Holland, P.W.2
-
42
-
-
29344441657
-
Animal evolution and the molecular signature of radiations compressed in time
-
Rokas A, Kruger D, Carroll SB. 2005. Animal evolution and the molecular signature of radiations compressed in time. Science 310:1933-1938.
-
(2005)
Science
, vol.310
, pp. 1933-1938
-
-
Rokas, A.1
Kruger, D.2
Carroll, S.B.3
-
43
-
-
43149098505
-
Rare genomic characters do not support Coelomata: RGC-CAMs
-
Roy SW, Irimia M. 2008. Rare genomic characters do not support Coelomata: RGC-CAMs. J Mol Evol. 66:308-315.
-
(2008)
J Mol Evol.
, vol.66
, pp. 308-315
-
-
Roy, S.W.1
Irimia, M.2
-
44
-
-
58849142045
-
Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis
-
Schierwater B, Eitel M, Jakob W, Osigus HJ, Hadrys H, Dellaporta SL, Kolokotronis SO, Desalle R. 2009. Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis. PLoS Biol. 7:e20.
-
(2009)
PLoS Biol.
, vol.7
-
-
Schierwater, B.1
Eitel, M.2
Jakob, W.3
Osigus, H.J.4
Hadrys, H.5
Dellaporta, S.L.6
Kolokotronis, S.O.7
Desalle, R.8
-
45
-
-
34447280568
-
The relative performance of indel-coding methods in simulations
-
Simmons MP, Muller K, Norton AP. 2007. The relative performance of indel-coding methods in simulations. Mol Phylogenet Evol. 44:724-740.
-
(2007)
Mol Phylogenet Evol
, vol.44
, pp. 724-740
-
-
Simmons, M.P.1
Muller, K.2
Norton, A.P.3
-
46
-
-
0034350427
-
Gaps as characters in sequence-based phylogenetic analyses
-
Simmons MP, Ochoterena H. 2000. Gaps as characters in sequence-based phylogenetic analyses. Syst Biol. 49:369-381.
-
(2000)
Syst Biol.
, vol.49
, pp. 369-381
-
-
Simmons, M.P.1
Ochoterena, H.2
-
47
-
-
0035527375
-
Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses
-
Simmons MP, Ochoterena H, Carr TG. 2001. Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses. Syst Biol. 50:454-462.
-
(2001)
Syst Biol.
, vol.50
, pp. 454-462
-
-
Simmons, M.P.1
Ochoterena, H.2
Carr, T.G.3
-
49
-
-
0042902833
-
The COG database: An updated version includes eukaryotes
-
(17 co-authors)
-
Tatusov RL, Fedorova ND, Jackson JD, et al. (17 co-authors). 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 41
-
-
Tatusov, R.L.1
Fedorova, N.D.2
Jackson, J.D.3
-
50
-
-
0021084212
-
Phylogenetic Inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes
-
Templeton AR. 1983. Phylogenetic Inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37:221-244.
-
(1983)
Evolution
, vol.37
, pp. 221-244
-
-
Templeton, A.R.1
-
51
-
-
0033085021
-
The virtues of gaps: Xenarthran (Edentate) monophyly supported by a unique deletion in alpha A-crystallin
-
van Dijk MAM, Paradis E, Catzeflis F, de Jong WW. 1999. The virtues of gaps: Xenarthran (Edentate) monophyly supported by a unique deletion in alpha A-crystallin. Syst Biol. 48:94-106.
-
(1999)
Syst Biol.
, vol.48
, pp. 94-106
-
-
Van Dijk, M.A.M.1
Paradis, E.2
Catzeflis, F.3
De Jong, W.W.4
-
52
-
-
59949096873
-
EnsemblCompara GeneTrees: Complete, duplication-aware phy-logenetic trees in vertebrates
-
Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E. 2009. EnsemblCompara GeneTrees: complete, duplication-aware phy-logenetic trees in vertebrates. Genome Res. 19:327-335.
-
(2009)
Genome Res.
, vol.19
, pp. 327-335
-
-
Vilella, A.J.1
Severin, J.2
Ureta-Vidal, A.3
Heng, L.4
Durbin, R.5
Birney, E.6
-
53
-
-
0345874732
-
Coelomata and not Ecdysozoa: Evidence from genome-wide phylogenetic analysis
-
Wolf YI, Rogozin IB, Koonin EV. 2004. Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. Genome Res. 14:29-36.
-
(2004)
Genome Res.
, vol.14
, pp. 29-36
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Koonin, E.V.3
-
54
-
-
33645769791
-
Large-scale trendsintheevolution of gene structures within 11 animal genomes
-
Yandell M, Mungall CJ, Smith C, Prochnik S, Kaminker J, Hartzell G, LewisS,RubinG, M. 2006. Large-scale trendsintheevolution of gene structures within 11 animal genomes. PLoS Comput Biol. 2:e15.
-
(2006)
PLoS Comput Biol.
, Issue.2
-
-
Yandell, M.1
Mungall, C.J.2
Smith, C.3
Prochnik, S.4
Kaminker, J.5
Hartzell, G.6
Lewis, S.7
Rubing, M.8
|