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Volumn 16, Issue 1, 2015, Pages

Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa

Author keywords

Ctenophora; Locus selection; Long branch attraction; Metazoa; Phylogenetic conflict; Phylogenomics

Indexed keywords

CNIDARIA; CTENOPHORA; GENOME; LONG BRANCH ATTRACTION; NERVE CELL; PLACOZOA; SISTER GROUP; STATISTICAL BIAS; WORKFLOW; ANIMAL; DATA MINING; GENE LOCUS; GENETICS; GENOMICS; HUMAN; MOLECULAR EVOLUTION; PHYLOGENY;

EID: 84947939166     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-2146-4     Document Type: Article
Times cited : (115)

References (69)
  • 2
    • 84884520631 scopus 로고    scopus 로고
    • Cnidarian-microbe interactions and the origin of innate immunity in metazoans
    • Bosch TC. Cnidarian-microbe interactions and the origin of innate immunity in metazoans. Annu Rev Microbiol. 2013;67:499-518. doi: 10.1146/annurev-micro-092412-155626.
    • (2013) Annu Rev Microbiol , vol.67 , pp. 499-518
    • Bosch, T.C.1
  • 3
    • 54149090863 scopus 로고    scopus 로고
    • The evolution of cell types in animals: emerging principles from molecular studies
    • Arendt D. The evolution of cell types in animals: emerging principles from molecular studies. Nat Rev Genet. 2008;9:868-82. doi: 10.1038/nrg2416.
    • (2008) Nat Rev Genet , vol.9 , pp. 868-882
    • Arendt, D.1
  • 4
    • 42149157760 scopus 로고    scopus 로고
    • Broad phylogenomic sampling improves resolution of the animal tree of life
    • Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, et al. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature. 2008;452:745-9.
    • (2008) Nature , vol.452 , pp. 745-749
    • Dunn, C.W.1    Hejnol, A.2    Matus, D.Q.3    Pang, K.4    Browne, W.E.5    Smith, S.A.6
  • 9
    • 84928974643 scopus 로고    scopus 로고
    • Error, signal, and the placement of Ctenophora sister to all other animals
    • Halanych KM, Whelan NV, Kocot KM, Moroz LL. Error, signal, and the placement of Ctenophora sister to all other animals. Proc Natl Acad Sci. 2015;112:5773-8. doi: 10.1073/pnas.1503453112.
    • (2015) Proc Natl Acad Sci , vol.112 , pp. 5773-5778
    • Halanych, K.M.1    Whelan, N.V.2    Kocot, K.M.3    Moroz, L.L.4
  • 10
    • 84890056203 scopus 로고    scopus 로고
    • NISC Comparative Sequencing Program, et al. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution
    • Ryan JF, Pang K, Schnitzler CE, Nguyen A-D, Moreland RT, Simmons DK, et al. NISC Comparative Sequencing Program, et al. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science. 2013;342:1242592.
    • (2013) Science , vol.342 , pp. 1242592
    • Ryan, J.F.1    Pang, K.2    Schnitzler, C.E.3    Nguyen, A.-D.4    Moreland, R.T.5    Simmons, D.K.6
  • 11
    • 84905024759 scopus 로고    scopus 로고
    • Did the ctenophore nervous system evolve independently?
    • Ryan JF. Did the ctenophore nervous system evolve independently? Zoology. 2013;117:225-6.
    • (2013) Zoology , vol.117 , pp. 225-226
    • Ryan, J.F.1
  • 13
    • 79953716259 scopus 로고    scopus 로고
    • Resolving difficult phylogenetic questions: why more sequences are not enough
    • Philippe H, Brinkmann H, Lavrov DV, Littlewood DTJ, Manuel M, Worheide G, et al. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol. 2011;9:e1000602. doi: 10.1371/journal.pbio.1000602.
    • (2011) PLoS Biol , vol.9 , pp. e1000602
    • Philippe, H.1    Brinkmann, H.2    Lavrov, D.V.3    Littlewood, D.T.J.4    Manuel, M.5    Worheide, G.6
  • 14
    • 67449163699 scopus 로고    scopus 로고
    • The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference
    • Lemmon AR, Brown JM, Stanger-Hall K, Lemmon EM. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Syst Biol. 2009;58:130-45.
    • (2009) Syst Biol , vol.58 , pp. 130-145
    • Lemmon, A.R.1    Brown, J.M.2    Stanger-Hall, K.3    Lemmon, E.M.4
  • 15
    • 84871842306 scopus 로고    scopus 로고
    • Impact of missing data on phylogenies inferred from empirical phylogenomic data sets
    • Roure B, Baurain D, Philippe H. Impact of missing data on phylogenies inferred from empirical phylogenomic data sets. Mol Biol Evol. 2013;30:197-214.
    • (2013) Mol Biol Evol , vol.30 , pp. 197-214
    • Roure, B.1    Baurain, D.2    Philippe, H.3
  • 16
    • 77955490196 scopus 로고
    • 2010. The Amphimedon queenslandica genome and the evolution of animal complexity
    • Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier MEA, Mitros T, et al. 2010. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature. 1938;466:720-6.
    • (1938) Nature , vol.466 , pp. 720-726
    • Srivastava, M.1    Simakov, O.2    Chapman, J.3    Fahey, B.4    Gauthier, M.E.A.5    Mitros, T.6
  • 17
    • 33645106540 scopus 로고    scopus 로고
    • OrthologID: automation of genome-scale ortholog identification within a parsimony framework
    • Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, DeSalle R. OrthologID: automation of genome-scale ortholog identification within a parsimony framework. Bioinformatics. 2006;22:699-707.
    • (2006) Bioinformatics , vol.22 , pp. 699-707
    • Chiu, J.C.1    Lee, E.K.2    Egan, M.G.3    Sarkar, I.N.4    Coruzzi, G.M.5    DeSalle, R.6
  • 18
    • 2442691520 scopus 로고    scopus 로고
    • A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
    • Lartillot N, Philippe H. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol. 2004;21:1095-109.
    • (2004) Mol Biol Evol , vol.21 , pp. 1095-1109
    • Lartillot, N.1    Philippe, H.2
  • 19
    • 34648836102 scopus 로고    scopus 로고
    • Draft genome of the filarial nematode parasite Brugia malayi
    • Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, et al. Draft genome of the filarial nematode parasite Brugia malayi. Science. 2007;317:1756-60. doi: 10.1126/science.1145406.
    • (2007) Science , vol.317 , pp. 1756-1760
    • Ghedin, E.1    Wang, S.2    Spiro, D.3    Caler, E.4    Zhao, Q.5    Crabtree, J.6
  • 20
    • 0032509302 scopus 로고    scopus 로고
    • C. elegans Sequencing Consortium Genome sequence of the nematode C. elegans: a platform for investigating biology
    • C. elegans Sequencing Consortium Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 1998;282:2012-2018
    • (1998) Science , vol.282 , pp. 2012-2018
  • 21
    • 81855212676 scopus 로고    scopus 로고
    • The genome of Tetranychus urticae reveals herbivorous pest adaptations
    • Grbic M, Van Leeuwen T, Clark RM, Rombauts S, Rouze P, Grbic V, et al. The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature. 2011;479:487-92. doi: 10.1038/nature10640.
    • (2011) Nature , vol.479 , pp. 487-492
    • Grbic, M.1    Leeuwen, T.2    Clark, R.M.3    Rombauts, S.4    Rouze, P.5    Grbic, V.6
  • 22
    • 78649705889 scopus 로고    scopus 로고
    • Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate
    • Denoeud F, Henriet S, Mungpakdee S, Aury JM, Da Silva C, Brinkmann H, et al. Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science. 2010;330:1381-5. doi: 10.1126/science.1194167.
    • (2010) Science , vol.330 , pp. 1381-1385
    • Denoeud, F.1    Henriet, S.2    Mungpakdee, S.3    Aury, J.M.4    Silva, C.5    Brinkmann, H.6
  • 23
    • 84950934893 scopus 로고
    • Raftery Bayes Factors
    • Kass R. Raftery Bayes Factors. J Am Stat Assoc. 1995;90:773-95.
    • (1995) J Am Stat Assoc , vol.90 , pp. 773-795
    • Kass, R.1
  • 24
    • 79951566251 scopus 로고    scopus 로고
    • Improving marginal likelihood estimation for Bayesian phylogenetic model selection
    • Xie W, Lewis PO, Fan Y, Kuo L, Chen MH. Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst Biol. 2011;60:150-60.
    • (2011) Syst Biol , vol.60 , pp. 150-160
    • Xie, W.1    Lewis, P.O.2    Fan, Y.3    Kuo, L.4    Chen, M.H.5
  • 25
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: a maximum likelihood approach
    • Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981;17:368-76.
    • (1981) J Mol Evol , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 26
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
    • Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312-3.
    • (2014) Bioinformatics , vol.30 , pp. 1312-1313
    • Stamatakis, A.1
  • 27
    • 0000228203 scopus 로고
    • A model ofevolutionary change in proteins
    • Dayhoff MO, editor. Atlas of protein sequence and structure, 3. Washington,DC: National Biomedical Research Foundation
    • Dayhoff MO, Schwartz RM, Orcutt BC. A model ofevolutionary change in proteins. In: Dayhoff MO, editor. Atlas of protein sequence and structure, 3. Washington,DC: National Biomedical Research Foundation; 1978. p. 345-52.
    • (1978) , pp. 345-352
    • Dayhoff, M.O.1    Schwartz, R.M.2    Orcutt, B.C.3
  • 28
    • 45849154166 scopus 로고    scopus 로고
    • An improved general amino acid replacement matrix
    • Le SQ, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol. 2008;25:1307-20.
    • (2008) Mol Biol Evol , vol.25 , pp. 1307-1320
    • Le, S.Q.1    Gascuel, O.2
  • 29
    • 17744386162 scopus 로고    scopus 로고
    • Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia
    • Philippe H, Lartillot N, Brinkmann H. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol Biol Evol. 2005;22:1246-53.
    • (2005) Mol Biol Evol , vol.22 , pp. 1246-1253
    • Philippe, H.1    Lartillot, N.2    Brinkmann, H.3
  • 30
    • 21344453544 scopus 로고    scopus 로고
    • Molecular phylogeny of the protochordates: chordate evolution
    • Zeng L, Swalla BJ. Molecular phylogeny of the protochordates: chordate evolution. Can J Zool. 2005;83:24-33.
    • (2005) Can J Zool , vol.83 , pp. 24-33
    • Zeng, L.1    Swalla, B.J.2
  • 32
    • 84878113118 scopus 로고    scopus 로고
    • Inferring ancient divergences requires genes with strong phylogenetic signals
    • Salichos L, Rokas A. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature. 2013;497:327-31.
    • (2013) Nature , vol.497 , pp. 327-331
    • Salichos, L.1    Rokas, A.2
  • 33
    • 84888788505 scopus 로고    scopus 로고
    • Selecting informative subsets of sparse supermatrices increases the chance to find correct trees
    • Misof B, Meyer B, von Reumont BM, Kück P, Misof K, Meusemann K. Selecting informative subsets of sparse supermatrices increases the chance to find correct trees. BMC Bioinformatics. 2013;14:348. doi: 10.1186/1471-2105-14-348.
    • (2013) BMC Bioinformatics , vol.14 , pp. 348
    • Misof, B.1    Meyer, B.2    Reumont, B.M.3    Kück, P.4    Misof, K.5    Meusemann, K.6
  • 34
    • 0032874259 scopus 로고    scopus 로고
    • The rooting of the universal tree of life is not reliable
    • Philippe H, Forterre P. The rooting of the universal tree of life is not reliable. J Mol Evol. 1999;49:509-23.
    • (1999) J Mol Evol , vol.49 , pp. 509-523
    • Philippe, H.1    Forterre, P.2
  • 35
    • 84898748138 scopus 로고    scopus 로고
    • TreSpEx-detection of misleading signal in phylogenetic reconstructions based on tree information
    • Struck TH. TreSpEx-detection of misleading signal in phylogenetic reconstructions based on tree information. Evol Bioinf. 2014;10:51-67.
    • (2014) Evol Bioinf , vol.10 , pp. 51-67
    • Struck, T.H.1
  • 36
    • 33845908745 scopus 로고
    • 2007. Lack of resolution in the animal phylogeny: closely spaced cladogeneses or undetected systematic errors
    • Baurain D, Brinkmann H, Philippe H. 2007. Lack of resolution in the animal phylogeny: closely spaced cladogeneses or undetected systematic errors. Mol Biol Evol. 1995;24:6-9.
    • (1995) Mol Biol Evol , vol.24 , pp. 6-9
    • Baurain, D.1    Brinkmann, H.2    Philippe, H.3
  • 37
    • 77952716890 scopus 로고    scopus 로고
    • Of mites and millipedes: recent progress in resolving the base of the arthropod tree
    • Caravas J, Friedrich M. Of mites and millipedes: recent progress in resolving the base of the arthropod tree. Bioessays. 2010;32:488-95. doi: 10.1002/bies.201000005.
    • (2010) Bioessays , vol.32 , pp. 488-495
    • Caravas, J.1    Friedrich, M.2
  • 38
    • 78650474944 scopus 로고    scopus 로고
    • A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata
    • Rota-Stabelli O, Campbell L, Brinkmann H, Edgecombe GD, Longhorn SJ, Peterson KJ, et al. A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata. Proc Royal Soc B. 2011;278(1703):298-306.
    • (2011) Proc Royal Soc B , vol.278 , Issue.1703 , pp. 298-306
    • Rota-Stabelli, O.1    Campbell, L.2    Brinkmann, H.3    Edgecombe, G.D.4    Longhorn, S.J.5    Peterson, K.J.6
  • 39
    • 84947908624 scopus 로고
    • Evolution of the annelida, onychophora and arthropoda, The Smithsonian Institution
    • Snodgrass RE. Evolution of the annelida, onychophora and arthropoda, The Smithsonian Institution. 1938.
    • (1938)
    • Snodgrass, R.E.1
  • 40
    • 77955950911 scopus 로고    scopus 로고
    • Compositional heterogeneity and phylogenomic inference of metazoan relationships
    • Nesnidal MP, Helmkampf M, Bruchhaus I, Hausdorf B. Compositional heterogeneity and phylogenomic inference of metazoan relationships. Mol Biol Evol. 2010;27:2095-104.
    • (2010) Mol Biol Evol , vol.27 , pp. 2095-2104
    • Nesnidal, M.P.1    Helmkampf, M.2    Bruchhaus, I.3    Hausdorf, B.4
  • 41
    • 3242701529 scopus 로고    scopus 로고
    • Modeling compositional heterogeneity
    • Foster PG. Modeling compositional heterogeneity. Syst Biol. 2004;53:485-95.
    • (2004) Syst Biol , vol.53 , pp. 485-495
    • Foster, P.G.1
  • 42
    • 47249122561 scopus 로고    scopus 로고
    • A site- and time-heterogeneous model of amino acid replacement
    • Blanquart S, Lartillot N. A site- and time-heterogeneous model of amino acid replacement. Mol Biol Evol. 2008;25:842-58.
    • (2008) Mol Biol Evol , vol.25 , pp. 842-858
    • Blanquart, S.1    Lartillot, N.2
  • 43
    • 84907482255 scopus 로고    scopus 로고
    • Strepsiptera, phylogenomics and the long branch attraction problem
    • Boussau B, Walton Z, Delgado JA, Collantes F, Beani L, Stewart IJ, et al. Strepsiptera, phylogenomics and the long branch attraction problem. PLoS One. 2014;9:e107709. doi: 10.1371/journal.pone.0107709.
    • (2014) PLoS One , vol.9 , pp. e107709
    • Boussau, B.1    Walton, Z.2    Delgado, J.A.3    Collantes, F.4    Beani, L.5    Stewart, I.J.6
  • 44
    • 20444491634 scopus 로고    scopus 로고
    • A review of long-branch attraction
    • Bergsten J. A review of long-branch attraction. Cladistics. 2005;21:163-93.
    • (2005) Cladistics , vol.21 , pp. 163-193
    • Bergsten, J.1
  • 45
    • 34248159030 scopus 로고    scopus 로고
    • Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model
    • Lartillot N, Brinkmann H, Philippe H. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol. 2007;7:S4. doi: 10.1186/1471-2148-7-S1-S4.
    • (2007) BMC Evol Biol , vol.7 , pp. S4
    • Lartillot, N.1    Brinkmann, H.2    Philippe, H.3
  • 46
    • 3042550872 scopus 로고    scopus 로고
    • Genome-scale phylogeny and the detection of systematic biases
    • Phillips MJ, Delsuc F, Penny D. Genome-scale phylogeny and the detection of systematic biases. Mol Biol Evol. 2004;21:1455-8.
    • (2004) Mol Biol Evol , vol.21 , pp. 1455-1458
    • Phillips, M.J.1    Delsuc, F.2    Penny, D.3
  • 47
    • 79955094039 scopus 로고    scopus 로고
    • The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa
    • Ryan JF, Pang K, Comparative Sequencing Program NISC, Mulkin JC, Martindale MQ, Baxevanis AD. The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa. EvoDevo. 2010;1:9. doi: 10.1186/2041-9139-1-9.
    • (2010) EvoDevo , vol.1 , pp. 9
    • Ryan, J.F.1    Pang, K.2    Comparative Sequencing Program, N.I.S.C.3    Mulkin, J.C.4    Martindale, M.Q.5    Baxevanis, A.D.6
  • 48
    • 0003633872 scopus 로고
    • Das System der Metazoa
    • Band I. Stuttgart, Germany: Fischer;
    • Ax P. Das System der Metazoa, Band I. Stuttgart, Germany: Fischer; 1995.
    • (1995)
    • Ax, P.1
  • 49
    • 58849142045 scopus 로고    scopus 로고
    • Concatenated analysis sheds light on early metazoan evolution and fuels a modern ;Urmetazoon; hypothesis
    • Schierwater B, Eitel M, Jakob W, Osigus H-J, Hadrys H, Dellaporta SL, et al. Concatenated analysis sheds light on early metazoan evolution and fuels a modern ;Urmetazoon; hypothesis. PLoS Biol. 2009;7:e1000020. doi: 10.1371/journal.pbio.1000020.
    • (2009) PLoS Biol , vol.7 , pp. e1000020
    • Schierwater, B.1    Eitel, M.2    Jakob, W.3    Osigus, H.-J.4    Hadrys, H.5    Dellaporta, S.L.6
  • 50
    • 0003643078 scopus 로고
    • The invertebrates. I. Protozoa through Coelenterata
    • New York: McGraw-Hill
    • Hyman L. The invertebrates. I. Protozoa through Coelenterata. New York: McGraw-Hill; 1940.
    • (1940)
    • Hyman, L.1
  • 51
    • 17744398025 scopus 로고    scopus 로고
    • More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy
    • Rokas A, Carroll SB. More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol Biol Evol. 2005;22:1337-44.
    • (2005) Mol Biol Evol , vol.22 , pp. 1337-1344
    • Rokas, A.1    Carroll, S.B.2
  • 52
    • 84947909119 scopus 로고    scopus 로고
    • developing community resources to study diverse invertebrate genomes
    • The Global Invertebrate Genomics Alliance (GIGA). developing community resources to study diverse invertebrate genomes. J Hered. 2014;105:1-18.
    • (2014) J Hered , vol.105 , pp. 1-18
  • 53
    • 84947992589 scopus 로고    scopus 로고
    • Employing phylogenomics to resolve the relationships among cnidarians, ctenophores, sponges, placozoans, and bilaterians
    • icv037
    • Whelan N. V., Kocot K. M. & Halanych K. M. Employing phylogenomics to resolve the relationships among cnidarians, ctenophores, sponges, placozoans, and bilaterians. Integr Comp Biol. 2015;icv037. doi: 10.1093/icb/icv037
    • (2015) Integr Comp Biol
    • Whelan, N.V.1    Kocot, K.M.2    Halanych, K.M.3
  • 54
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002;30:1575-84.
    • (2002) Nucleic Acids Res , vol.30 , pp. 1575-1584
    • Enright, A.J.1    Dongen, S.2    Ouzounis, C.A.3
  • 55
    • 61849113253 scopus 로고    scopus 로고
    • Graph clustering via a discrete uncoupling process
    • Van Dongen S. Graph clustering via a discrete uncoupling process. SIAM J Matrix Anal Appl. 2008;30:121-41.
    • (2008) SIAM J Matrix Anal Appl , vol.30 , pp. 121-141
    • Dongen, S.1
  • 56
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792-7.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 57
    • 67650757433 scopus 로고    scopus 로고
    • TrimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
    • Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. TrimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972-3. doi: 10.1093/bioinformatics/btp348.
    • (2009) Bioinformatics , vol.25 , pp. 1972-1973
    • Capella-Gutiérrez, S.1    Silla-Martínez, J.M.2    Gabaldón, T.3
  • 58
    • 43949138227 scopus 로고    scopus 로고
    • Blast2GO: A comprehensive suite for functional analysis in plant genomics
    • Conesa A, Gotz S. Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics. 2008;2008:619832. doi: 10.1155/2008/619832.
    • (2008) Int J Plant Genomics , vol.2008 , pp. 619832
    • Conesa, A.1    Gotz, S.2
  • 59
    • 77954299992 scopus 로고    scopus 로고
    • agriGO: a GO analysis toolkit for the agricultural community
    • Du Z, Zhou X, Ling Y, Zhang Z, Su Z. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 2010;38:W64-70. doi: 10.1093/nar/gkq310.
    • (2010) Nucleic Acids Res , vol.38 , pp. W64-70
    • Du, Z.1    Zhou, X.2    Ling, Y.3    Zhang, Z.4    Su, Z.5
  • 60
    • 79960610118 scopus 로고    scopus 로고
    • REVIGO summarizes and visualizes long lists of Gene Ontology terms
    • Supek F, Bošnjak M, Škunca N, Šmuc T. REVIGO summarizes and visualizes long lists of Gene Ontology terms; PLoS ONE 2011. doi:10.1371/journal.pone.0021800
    • (2011) PLoS ONE
    • Supek, F.1    Bošnjak, M.2    Škunca, N.3    Šmuc, T.4
  • 61
    • 40049112246 scopus 로고    scopus 로고
    • Phyutility: a phyloinformatics tool for trees, alignments, and molecular data
    • Smith SA, Dunn CW. Phyutility: a phyloinformatics tool for trees, alignments, and molecular data. Bioinformatics. 2008;24:715-6.
    • (2008) Bioinformatics , vol.24 , pp. 715-716
    • Smith, S.A.1    Dunn, C.W.2
  • 62
    • 3042649996 scopus 로고    scopus 로고
    • Mesquite: A modular system for evolutionary analysis
    • v2.75 [WWW document] URL [accessed on 1 January ]
    • Maddison WP, Maddison DR. Mesquite: A modular system for evolutionary analysis. v2.75 [WWW document] URL http://mesquiteproject.org/ [accessed on 1 January 2013]
    • (2013)
    • Maddison, W.P.1    Maddison, D.R.2
  • 63
    • 41149089793 scopus 로고    scopus 로고
    • SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis in Structural approaches to sequence evolution: Molecules, networks, populations
    • (U. Bastolla, M. Porto, H.E. Roman and M. Vendruscolo Eds.) Biological and Medical Physics, Biomedical Engineering
    • Charif D, Lobry JR. SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis in Structural approaches to sequence evolution: Molecules, networks, populations (U. Bastolla, M. Porto, H.E. Roman and M. Vendruscolo Eds.) Biological and Medical Physics, Biomedical Engineering; 2007. pp 207-232.
    • (2007) , pp. 207-232
    • Charif, D.1    Lobry, J.R.2
  • 64
    • 1042304216 scopus 로고    scopus 로고
    • APE: Analyses of phylogenetics and evolution in R language
    • Paradis E, Claude J, Strimmer K. APE: Analyses of phylogenetics and evolution in R language. Bioinformatics. 2004;20:289-90.
    • (2004) Bioinformatics , vol.20 , pp. 289-290
    • Paradis, E.1    Claude, J.2    Strimmer, K.3
  • 65
    • 84900407539 scopus 로고    scopus 로고
    • Selecting optimal partitioning schemes for phylogenomic datasets
    • Lanfear R, Calcott B, Kainer D, Mayer C, Stamatakis A. Selecting optimal partitioning schemes for phylogenomic datasets. BMC Evol Biol. 2014;14:82. doi: 10.1186/1471-2148-14-82.
    • (2014) BMC Evol Biol , vol.14 , pp. 82
    • Lanfear, R.1    Calcott, B.2    Kainer, D.3    Mayer, C.4    Stamatakis, A.5
  • 66
    • 84881629698 scopus 로고    scopus 로고
    • PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment
    • Lartillot N, Rodrigue N, Stubbs D, Richer J. PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst Biol. 2013;62:611-5.
    • (2013) Syst Biol , vol.62 , pp. 611-615
    • Lartillot, N.1    Rodrigue, N.2    Stubbs, D.3    Richer, J.4
  • 67
    • 69949126557 scopus 로고    scopus 로고
    • PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
    • Lartillot N, Lepage T, Blanquart S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics. 2009;25:2286-8.
    • (2009) Bioinformatics , vol.25 , pp. 2286-2288
    • Lartillot, N.1    Lepage, T.2    Blanquart, S.3
  • 68
    • 85016784086 scopus 로고    scopus 로고
    • Mcmcplots: create plots from MCMC output
    • R package version 0.4.1.
    • Curtis SM. Mcmcplots: create plots from MCMC output. R package version 0.4.1. http://CRAN.R-project.org/package=mcmcplots.
    • Curtis, S.M.1
  • 69
    • 84860109324 scopus 로고    scopus 로고
    • MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space
    • Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012;61:539-42.
    • (2012) Syst Biol , vol.61 , pp. 539-542
    • Ronquist, F.1    Teslenko, M.2    Mark, P.3    Ayres, D.L.4    Darling, A.5    Höhna, S.6


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