-
1
-
-
18844435622
-
Myzostomida: A review of the phylogeny and ultrastructure
-
Eeckhaut I, Lanterbecq D, (2005) Myzostomida: A review of the phylogeny and ultrastructure. Hydrobiologia 535: 253-275.
-
(2005)
Hydrobiologia
, vol.535
, pp. 253-275
-
-
Eeckhaut, I.1
Lanterbecq, D.2
-
2
-
-
73149125552
-
Evidence for cospeciation events in the host-symbiont system involving crinoids (echinodermata) and their obligate associates, the myzostomids (myzostomida, annelida)
-
Lanterbecq D, Rouse GW, Eeckhaut I, (2010) Evidence for cospeciation events in the host-symbiont system involving crinoids (echinodermata) and their obligate associates, the myzostomids (myzostomida, annelida). Mol Phylogenet Evol 54: 357-71.
-
(2010)
Mol Phylogenet Evol
, vol.54
, pp. 357-371
-
-
Lanterbecq, D.1
Rouse, G.W.2
Eeckhaut, I.3
-
3
-
-
34547812067
-
Mitochondrial genome and nuclear sequence data support myzostomida as part of the annelid radiation
-
Bleidorn C, Eeckhaut I, Podsiadlowski L, Schult N, McHugh D, et al. (2007) Mitochondrial genome and nuclear sequence data support myzostomida as part of the annelid radiation. Mol Biol Evol 24: 1690-1701.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1690-1701
-
-
Bleidorn, C.1
Eeckhaut, I.2
Podsiadlowski, L.3
Schult, N.4
McHugh, D.5
-
4
-
-
67849135832
-
On the phylogenetic position of myzostomida: Can 77 genes get it wrong
-
Bleidorn C, Podsiadlowski L, Zhong M, Eeckhaut I, Hartmann S, et al. (2009) On the phylogenetic position of myzostomida: Can 77 genes get it wrong. BMC Evol Biol 9.
-
(2009)
BMC Evol Biol
, vol.9
-
-
Bleidorn, C.1
Podsiadlowski, L.2
Zhong, M.3
Eeckhaut, I.4
Hartmann, S.5
-
5
-
-
67349117809
-
A pcr survey of hox genes in the myzostomid Myzostoma cirriferum
-
Bleidorn C, Lanterbecq D, Eeckhaut I, Tiedemann R, (2009) A pcr survey of hox genes in the myzostomid Myzostoma cirriferum. Dev Genes Evol 219: 211-216.
-
(2009)
Dev Genes Evol
, vol.219
, pp. 211-216
-
-
Bleidorn, C.1
Lanterbecq, D.2
Eeckhaut, I.3
Tiedemann, R.4
-
6
-
-
0034702477
-
Myzostomida: a link between trochozoans and flatworms?
-
Eeckhaut I, McHugh D, Mardulyn P, Tiedemann R, Monteyne D, et al. (2000) Myzostomida: a link between trochozoans and flatworms? Proc Biol Sci 267: 1383-1392.
-
(2000)
Proc Biol Sci
, vol.267
, pp. 1383-1392
-
-
Eeckhaut, I.1
McHugh, D.2
Mardulyn, P.3
Tiedemann, R.4
Monteyne, D.5
-
7
-
-
42149157760
-
Broad phylogenomic sampling improves resolution of the animal tree of life
-
Dunn C, Hejnol A, Matus D, Pang K, Browne W, et al. (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.1
Hejnol, A.2
Matus, D.3
Pang, K.4
Browne, W.5
-
8
-
-
72749099971
-
Assessing the root of bilaterian animals with scalable phylogenomic methods
-
Hejnol A, Obst M, Stamatakis A, Ott M, Rouse GW, et al. (2009) Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc Biol Sci 276: 4261-70.
-
(2009)
Proc Biol Sci
, vol.276
, pp. 4261-4270
-
-
Hejnol, A.1
Obst, M.2
Stamatakis, A.3
Ott, M.4
Rouse, G.W.5
-
9
-
-
64849090758
-
Lophotrochozoa internal phylogeny: new insights from an up-to-date analysis of nuclear ribosomal genes
-
Paps J, Baguñà J, Riutort M, (2009) Lophotrochozoa internal phylogeny: new insights from an up-to-date analysis of nuclear ribosomal genes. Proc Biol Sci 276: 1245-54.
-
(2009)
Proc Biol Sci
, vol.276
, pp. 1245-1254
-
-
Paps, J.1
Baguñà, J.2
Riutort, M.3
-
10
-
-
79952254741
-
Phylogenomic analyses unravel annelid evolution
-
Struck TH, Paul C, Hill N, Hartmann S, Hösel C, et al. (2011) Phylogenomic analyses unravel annelid evolution. Nature 471: 95-8.
-
(2011)
Nature
, vol.471
, pp. 95-98
-
-
Struck, T.H.1
Paul, C.2
Hill, N.3
Hartmann, S.4
Hösel, C.5
-
11
-
-
65249099546
-
Phylogenomics revives traditional views on deep animal relationships
-
Philippe H, Derelle R, Lopez P, Pick K, Borchiellini C, et al. (2009) Phylogenomics revives traditional views on deep animal relationships. Curr Biol 19: 706-12.
-
(2009)
Curr Biol
, vol.19
, pp. 706-712
-
-
Philippe, H.1
Derelle, R.2
Lopez, P.3
Pick, K.4
Borchiellini, C.5
-
12
-
-
0033692378
-
Notung: A program for dating gene duplications and optimizing gene family trees
-
Chen K, Durand D, Farach-Colton M, (2000) Notung: A program for dating gene duplications and optimizing gene family trees. Journal of Computational Biology 7: 429-447.
-
(2000)
Journal of Computational Biology
, vol.7
, pp. 429-447
-
-
Chen, K.1
Durand, D.2
Farach-Colton, M.3
-
13
-
-
0034791426
-
A simple algorithm to infer gene duplication and speciation events on a gene tree
-
Zmasek C, Eddy S, (2001) A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics 17: 821-828.
-
(2001)
Bioinformatics
, vol.17
, pp. 821-828
-
-
Zmasek, C.1
Eddy, S.2
-
14
-
-
33746433923
-
Optimal gene trees from sequences and species trees using a soft interpretation of parsimony
-
Berglund-Sonnhammer A, Steffansson P, Betts M, Liberles D, (2006) Optimal gene trees from sequences and species trees using a soft interpretation of parsimony. J Mol Evol 63: 240-250.
-
(2006)
J Mol Evol
, vol.63
, pp. 240-250
-
-
Berglund-Sonnhammer, A.1
Steffansson, P.2
Betts, M.3
Liberles, D.4
-
15
-
-
84856030627
-
Chapter 5: Tangled tales from multiple markers
-
In: Bininda-Emonds ORP, editors, Combining information to reveal the Tree of Life, Kluwer Academic Publishers
-
Cotton JA, Page RDM, (2004) Chapter 5: Tangled tales from multiple markers. In: Bininda-Emonds ORP, editors. Phylogenetic Supertrees Combining information to reveal the Tree of Life, Kluwer Academic Publishers pp. 107-125.
-
(2004)
Phylogenetic Supertrees
, pp. 107-125
-
-
Cotton, J.A.1
Page, R.D.M.2
-
16
-
-
0000365320
-
Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences
-
Goodman M, Czelusniak J, Moore GW, Romero-Herrera AE, Matsuda G, (1979) Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Systematic Zoology 28: 132-163.
-
(1979)
Systematic Zoology
, vol.28
, pp. 132-163
-
-
Goodman, M.1
Czelusniak, J.2
Moore, G.W.3
Romero-Herrera, A.E.4
Matsuda, G.5
-
17
-
-
79951569533
-
Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees
-
Burleigh JG, Bansal MS, Eulenstein O, Hartmann S, Wehe A, et al. (2011) Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees. Syst Biol 60: 117-25.
-
(2011)
Syst Biol
, vol.60
, pp. 117-125
-
-
Burleigh, J.G.1
Bansal, M.S.2
Eulenstein, O.3
Hartmann, S.4
Wehe, A.5
-
18
-
-
77958450862
-
Deep genomic-scale analyses of the metazoa reject coelomata: evidence from single- and multigene families analyzed under a supertree and supermatrix paradigm
-
Holton TA, Pisani D, (2010) Deep genomic-scale analyses of the metazoa reject coelomata: evidence from single- and multigene families analyzed under a supertree and supermatrix paradigm. Genome Biol Evol 2: 310-24.
-
(2010)
Genome Biol Evol
, vol.2
, pp. 310-324
-
-
Holton, T.A.1
Pisani, D.2
-
19
-
-
77956285690
-
Illumina sequencing library preparation for highly multiplexed target capture and sequencing
-
Meyer M, Kircher M, (2010) Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc 2010: pdb.prot5448.
-
(2010)
Cold Spring Harb Protoc 2010: Pdb.prot5448
-
-
Meyer, M.1
Kircher, M.2
-
20
-
-
70350023532
-
Improved base calling for the illumina genome analyzer using machine learning strategies
-
Kircher M, Stenzel U, Kelso J, (2009) Improved base calling for the illumina genome analyzer using machine learning strategies. Genome Biol 10: R83.
-
(2009)
Genome Biol
, vol.10
-
-
Kircher, M.1
Stenzel, U.2
Kelso, J.3
-
21
-
-
79960852002
-
Addressing challenges in the production and analysis of illumina sequencing data
-
Kircher M, Heyn P, Kelso J, (2011) Addressing challenges in the production and analysis of illumina sequencing data. BMC Genomics 12: 382.
-
(2011)
BMC Genomics
, vol.12
, pp. 382
-
-
Kircher, M.1
Heyn, P.2
Kelso, J.3
-
22
-
-
18644368714
-
The bioperl toolkit: Perl modules for the life sciences
-
Stajich J, Block D, Boulez K, Brenner S, Chervitz S, et al. (2002) The bioperl toolkit: Perl modules for the life sciences. Genome Research 12: 1611-1618.
-
(2002)
Genome Research
, vol.12
, pp. 1611-1618
-
-
Stajich, J.1
Block, D.2
Boulez, K.3
Brenner, S.4
Chervitz, S.5
-
23
-
-
0025183708
-
Basic local alignment search tool
-
Altschul S, Gish W, Miller W, Myers E, Lipman D, (1990) Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
-
(1990)
Journal of Molecular Biology
, vol.215
, pp. 403-410
-
-
Altschul, S.1
Gish, W.2
Miller, W.3
Myers, E.4
Lipman, D.5
-
24
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
Enright A, Van Dongen S, Ouzounis C, (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Research 30: 1575-1584.
-
(2002)
Nucleic Acids Research
, vol.30
, pp. 1575-1584
-
-
Enright, A.1
Van Dongen, S.2
Ouzounis, C.3
-
26
-
-
40549098736
-
Uniprotkb/swiss-prot: The manually annotated section of the uniprot knowledgebase
-
Boutet E, Lieberherr D, Tognolli M, Schneider M, Bairoch A, (2007) Uniprotkb/swiss-prot: The manually annotated section of the uniprot knowledgebase. Methods Mol Biol 406: 89-112.
-
(2007)
Methods Mol Biol
, vol.406
, pp. 89-112
-
-
Boutet, E.1
Lieberherr, D.2
Tognolli, M.3
Schneider, M.4
Bairoch, A.5
-
27
-
-
38549097071
-
The universal protein resource (uniprot)
-
UniProtConsortium
-
UniProtConsortium (2008) The universal protein resource (uniprot). Nucleic Acids Res 36: D190-5.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
-
28
-
-
13744252890
-
Mafft version 5: improvement in accuracy of multiple sequence alignment
-
Katoh K, Kuma K, Toh H, Miyata T, (2005) Mafft version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research 33: 511-518.
-
(2005)
Nucleic Acids Research
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
Miyata, T.4
-
29
-
-
0035861990
-
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
-
Remm M, Storm CE, Sonnhammer EL, (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 314: 1041-52.
-
(2001)
J Mol Biol
, vol.314
, pp. 1041-1052
-
-
Remm, M.1
Storm, C.E.2
Sonnhammer, E.L.3
-
30
-
-
14644397888
-
Raxml-iii: a fast program for maximum likelihood-based inference of large phylogenetic trees
-
Stamatakis A, Ludwig T, Meier H, (2005) Raxml-iii: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21: 456-463.
-
(2005)
Bioinformatics
, vol.21
, pp. 456-463
-
-
Stamatakis, A.1
Ludwig, T.2
Meier, H.3
-
31
-
-
40049112246
-
Phyutility: a phyloinformatics tool for trees, alignments and molecular data
-
Smith SA, Dunn CW, (2008) Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 24: 715-6.
-
(2008)
Bioinformatics
, vol.24
, pp. 715-716
-
-
Smith, S.A.1
Dunn, C.W.2
-
32
-
-
43249090276
-
Using ests for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?
-
Hartmann S, Vision T, (2008) Using ests for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment? BMC Evol Biol 8: 95.
-
(2008)
BMC Evol Biol
, vol.8
, pp. 95
-
-
Hartmann, S.1
Vision, T.2
-
33
-
-
0031296691
-
Inferring species trees from gene trees: A phylogenetic analysis of the elapidae (serpentes) based on the amino acid sequences of venom proteins
-
Slowinski JB, Knight A, Rooney AP, (1997) Inferring species trees from gene trees: A phylogenetic analysis of the elapidae (serpentes) based on the amino acid sequences of venom proteins. Molecular Phylogenetics and Evolution 8: 349-362.
-
(1997)
Molecular Phylogenetics and Evolution
, vol.8
, pp. 349-362
-
-
Slowinski, J.B.1
Knight, A.2
Rooney, A.P.3
-
34
-
-
0031504952
-
Gene trees in species trees
-
Maddison WP, (1997) Gene trees in species trees. Systematic Biology 46: 523-536.
-
(1997)
Systematic Biology
, vol.46
, pp. 523-536
-
-
Maddison, W.P.1
-
35
-
-
46249126320
-
Duptree: a program for large-scale phylogenetic analyses using gene tree parsimony
-
Wehe A, Bansal M, Burleigh J, Eulenstein O, (2008) Duptree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics 24: 1540-1541.
-
(2008)
Bioinformatics
, vol.24
, pp. 1540-1541
-
-
Wehe, A.1
Bansal, M.2
Burleigh, J.3
Eulenstein, O.4
-
36
-
-
0027846270
-
Life cycle and mode of infestation of Myzostoma cirriferum (annelida), a symbiotic myzostomid of the comatulid crinoid Antedon bifida (echinodermata)
-
Eeckhaut I, Jangoux M, (1993) Life cycle and mode of infestation of Myzostoma cirriferum (annelida), a symbiotic myzostomid of the comatulid crinoid Antedon bifida (echinodermata). Diseases of Aquatic Organisms 15: 207-217.
-
(1993)
Diseases of Aquatic Organisms
, vol.15
, pp. 207-217
-
-
Eeckhaut, I.1
Jangoux, M.2
-
37
-
-
0242365676
-
Genome-scale approaches to resolving incongruence in molecular phylogenies
-
Rokas A, Williams B, King N, Carroll S, (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
-
38
-
-
3242703950
-
A molecular supermatrix of the rabbits and hares (leporidae) allows for the identification of five intercontinental exchanges during the miocene
-
Matthee CA, van Vuuren BJ, Bell D, Robinson TJ, (2004) A molecular supermatrix of the rabbits and hares (leporidae) allows for the identification of five intercontinental exchanges during the miocene. Syst Biol 53: 433-47.
-
(2004)
Syst Biol
, vol.53
, pp. 433-447
-
-
Matthee, C.A.1
van Vuuren, B.J.2
Bell, D.3
Robinson, T.J.4
-
39
-
-
77958144939
-
A phylogenomic approach to resolve the arthropod tree of life
-
Meusemann K, von Reumont BM, Simon S, Roeding F, Strauss S, et al. (2010) A phylogenomic approach to resolve the arthropod tree of life. Mol Biol Evol 27: 2451-64.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 2451-2464
-
-
Meusemann, K.1
von Reumont, B.M.2
Simon, S.3
Roeding, F.4
Strauss, S.5
-
40
-
-
33645850710
-
Phylogenomics: the beginning of incongruence?
-
Jeffroy O, Brinkmann H, Delsuc F, Philippe H, (2006) Phylogenomics: the beginning of incongruence? Trends Genet 22: 225-231.
-
(2006)
Trends Genet
, vol.22
, pp. 225-231
-
-
Jeffroy, O.1
Brinkmann, H.2
Delsuc, F.3
Philippe, H.4
-
41
-
-
0033278654
-
How should species phylogenies be inferred from sequence data?
-
Slowinski JB, Page RD, (1999) How should species phylogenies be inferred from sequence data? Syst Biol 48: 814-25.
-
(1999)
Syst Biol
, vol.48
, pp. 814-825
-
-
Slowinski, J.B.1
Page, R.D.2
-
42
-
-
0031296691
-
Inferring species trees from gene trees: A phylogenetic analysis of the elapidae (serpentes) based on the amino acid sequences of venom proteins
-
Slowinski JB, Knight A, Rooney AP, (1997) Inferring species trees from gene trees: A phylogenetic analysis of the elapidae (serpentes) based on the amino acid sequences of venom proteins. Molecular Phylogenetics and Evolution 8: 349-362.
-
(1997)
Molecular Phylogenetics and Evolution
, vol.8
, pp. 349-362
-
-
Slowinski, J.B.1
Knight, A.2
Rooney, A.P.3
-
43
-
-
0037036630
-
Going nuclear: gene family evolution and vertebrate phylogeny reconciled
-
Cotton JA, Page RDM, (2002) Going nuclear: gene family evolution and vertebrate phylogeny reconciled. Proc Biol Sci 269: 1555-61.
-
(2002)
Proc Biol Sci
, vol.269
, pp. 1555-1561
-
-
Cotton, J.A.1
Page, R.D.M.2
-
44
-
-
84856030627
-
Chapter 5: Tangled tales from multiple markers
-
In: Bininda-Emonds ORP, editors, Combining information to reveal the Tree of Life, Kluwer Academic Publishers
-
Cotton JA, Page RDM, (2004) Chapter 5: Tangled tales from multiple markers. In: Bininda-Emonds ORP, editors. Phylogenetic Supertrees Combining information to reveal the Tree of Life, Kluwer Academic Publishers pp. 107-125.
-
(2004)
Phylogenetic Supertrees
, pp. 107-125
-
-
Cotton, J.A.1
Page, R.D.M.2
-
45
-
-
0036365666
-
Vertebrate phylogenomics: reconciled trees and gene duplications
-
Page RDM, Cotton JA, (2002) Vertebrate phylogenomics: reconciled trees and gene duplications. Pac Symp Biocomput pp. 536-47.
-
(2002)
Pac Symp Biocomput
, pp. 536-547
-
-
Page, R.D.M.1
Cotton, J.A.2
-
46
-
-
1642274782
-
Gene tree parsimony vs uninode coding for phylogenetic reconstruction
-
Cotton JA, Page RDM, (2003) Gene tree parsimony vs uninode coding for phylogenetic reconstruction. Mol Phylogenet Evol 29: 298-308.
-
(2003)
Mol Phylogenet Evol
, vol.29
, pp. 298-308
-
-
Cotton, J.A.1
Page, R.D.M.2
-
47
-
-
34248217100
-
Inferring angiosperm phylogeny from est data with widespread gene duplication
-
Sanderson M, McMahon M, (2007) Inferring angiosperm phylogeny from est data with widespread gene duplication. BMC Evol Biol 7 (Suppl 1): S3.
-
(2007)
BMC Evol Biol
, vol.7
, Issue.SUPPL. 1
-
-
Sanderson, M.1
McMahon, M.2
-
48
-
-
78650722451
-
A.: Heuristics for the gene duplication problem: A θ (n) speed-up for the local search
-
Bansal MS, Burleigh JG, Eulenstein O, Wehe A, (2007) A.: Heuristics for the gene duplication problem: A θ (n) speed-up for the local search. RECOMB 2007: 238-252.
-
(2007)
RECOMB
, vol.2007
, pp. 238-252
-
-
Bansal, M.S.1
Burleigh, J.G.2
Eulenstein, O.3
Wehe, A.4
-
49
-
-
75149135738
-
Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models
-
Bansal MS, Burleigh JG, Eulenstein O, (2010) Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models. BMC Bioinformatics 11 (Suppl 1): S42.
-
(2010)
BMC Bioinformatics
, vol.11
, Issue.SUPPL. 1
-
-
Bansal, M.S.1
Burleigh, J.G.2
Eulenstein, O.3
|