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Volumn 13, Issue 4, 2014, Pages 1255-1258

siMBa—a simple graphical user interface for the Bayesian phylogenetic inference program MrBayes

Author keywords

Bayesian inference; Graphical user interface; MrBayes; Perl; Phylogenetic analysis software; Tk

Indexed keywords


EID: 84909993306     PISSN: 1617416X     EISSN: 18618952     Source Type: Journal    
DOI: 10.1007/s11557-014-1010-2     Document Type: Article
Times cited : (30)

References (23)
  • 2
    • 84864453108 scopus 로고    scopus 로고
    • jModelTest 2: more models, new heuristics and parallel computing
    • PID: 22847109, COI: 1:CAS:528:DC%2BC38XhtFWmsbfP
    • Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772
    • (2012) Nat Methods , vol.9 , pp. 772
    • Darriba, D.1    Taboada, G.L.2    Doallo, R.3    Posada, D.4
  • 4
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA-sequences—a maximum-likelihood approach
    • PID: 7288891, COI: 1:CAS:528:DyaL3MXls1Cisr8%3D
    • Felsenstein J (1981) Evolutionary trees from DNA-sequences—a maximum-likelihood approach. J Mol Evol 17:368–376
    • (1981) J Mol Evol , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 6
    • 74549125386 scopus 로고    scopus 로고
    • SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building
    • PID: 19854763, COI: 1:CAS:528:DC%2BC3cXntlGgtw%3D%3D
    • Gouy M, Guindon S, Gascuel O (2010) SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27:221–224
    • (2010) Mol Biol Evol , vol.27 , pp. 221-224
    • Gouy, M.1    Guindon, S.2    Gascuel, O.3
  • 7
    • 77956890234 scopus 로고
    • Monte Carlo sampling methods using Markov chains and their applications
    • Hastings WK (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57:97–109
    • (1970) Biometrika , vol.57 , pp. 97-109
    • Hastings, W.K.1
  • 8
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • PID: 11524383, COI: 1:STN:280:DC%2BD3MvotV2isw%3D%3D
    • Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 9
    • 0035861456 scopus 로고    scopus 로고
    • Evolution—Bayesian inference of phylogeny and its impact on evolutionary biology
    • PID: 11743192, COI: 1:CAS:528:DC%2BD3MXptFGkt7k%3D
    • Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP (2001) Evolution—Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310–2314
    • (2001) Science , vol.294 , pp. 2310-2314
    • Huelsenbeck, J.P.1    Ronquist, F.2    Nielsen, R.3    Bollback, J.P.4
  • 10
    • 0034894308 scopus 로고    scopus 로고
    • T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks
    • PID: 11448889, COI: 1:CAS:528:DC%2BD3MXmtleltL0%3D
    • Makarenkov U (2001) T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks. Bioinformatics 17:664–668
    • (2001) Bioinformatics , vol.17 , pp. 664-668
    • Makarenkov, U.1
  • 11
    • 0031498410 scopus 로고    scopus 로고
    • Phylogenetic inference for binary data on dendograms using Markov chain Monte Carlo
    • Mau B, Newton MA (1997) Phylogenetic inference for binary data on dendograms using Markov chain Monte Carlo. J Comput Graph Stat 6:122–131
    • (1997) J Comput Graph Stat , vol.6 , pp. 122-131
    • Mau, B.1    Newton, M.A.2
  • 12
    • 0032906031 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference via Markov chain Monte Carlo methods
    • PID: 11318142, COI: 1:STN:280:DC%2BD3M3ntV2qsw%3D%3D
    • Mau B, Newton MA, Larget B (1999) Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics 55:1–12
    • (1999) Biometrics , vol.55 , pp. 1-12
    • Mau, B.1    Newton, M.A.2    Larget, B.3
  • 14
    • 78751558547 scopus 로고    scopus 로고
    • (2010) Creating the CIPRES science gateway for inference of large phylogenetic trees. Proceedings of the Gateway Computing Environments Workshop, New Orleans
    • Miller MA, Pfeiffer W, Schwartz T (2010) Creating the CIPRES science gateway for inference of large phylogenetic trees. Proceedings of the Gateway Computing Environments Workshop, New Orleans, LA, 14 Nov 2010, pp 1–8
    • (2010) LA , vol.14 , pp. 1-8
    • Miller, M.A.1    Pfeiffer, W.2    Schwartz, T.3
  • 15
    • 58049218990 scopus 로고    scopus 로고
    • TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops
    • PID: 18984599, COI: 1:CAS:528:DC%2BD1MXmvFaq
    • Milne I, Lindner D, Bayer M, Husmeier D, McGuire G, Marshall DF, Wright F (2009) TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Bioinformatics 25:126–127
    • (2009) Bioinformatics , vol.25 , pp. 126-127
    • Milne, I.1    Lindner, D.2    Bayer, M.3    Husmeier, D.4    McGuire, G.5    Marshall, D.F.6    Wright, F.7
  • 16
    • 84909995793 scopus 로고    scopus 로고
    • Roderic DM (2008) The Santos Lab. University of Glasgow. Accessed 30 Mar 2014
    • Roderic DM (2008) The Santos Lab. University of Glasgow. http://www.auburn.edu/~santosr/mrbayesform.htm. Accessed 30 Mar 2014
  • 17
    • 0026660413 scopus 로고
    • A simple method for estimating and testing minimum-evolution trees
    • COI: 1:CAS:528:DyaK38Xls1KhsL0%3D
    • Rzhetsky A, Nei M (1992) A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 9:945–967
    • (1992) Mol Biol Evol , vol.9 , pp. 945-967
    • Rzhetsky, A.1    Nei, M.2
  • 18
    • 0000130363 scopus 로고
    • The neighbor-joining method—a new method for reconstructing phylogenetic trees
    • Saitou N, Nei M (1986) The neighbor-joining method—a new method for reconstructing phylogenetic trees. Jpn J Genet 61:611
    • (1986) Jpn J Genet , vol.61 , pp. 611
    • Saitou, N.1    Nei, M.2
  • 19
    • 0023375195 scopus 로고
    • The neighbor-joining method—a new method for reconstructing phylogenetic trees
    • PID: 3447015, COI: 1:STN:280:DyaL1c7ovFSjsA%3D%3D
    • Saitou N, Nei M (1987) The neighbor-joining method—a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    • (1987) Mol Biol Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 20
    • 84860434973 scopus 로고    scopus 로고
    • raxmlGUI: a graphical front-end for RAxML
    • Silvestro D, Michalak I (2012) raxmlGUI: a graphical front-end for RAxML. Org Divers Evol 12(4):335–337
    • (2012) Org Divers Evol , vol.12 , Issue.4 , pp. 335-337
    • Silvestro, D.1    Michalak, I.2
  • 21
    • 50249100595 scopus 로고    scopus 로고
    • A rapid bootstrap algorithm for the RAxML web servers
    • PID: 18853362
    • Stamatakis A, Hoover P, Rougemont J (2008) A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 57:758–771
    • (2008) Syst Biol , vol.57 , pp. 758-771
    • Stamatakis, A.1    Hoover, P.2    Rougemont, J.3
  • 22
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • PID: 21546353, COI: 1:CAS:528:DC%2BC3MXht1eiu73K
    • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
    • (2011) Mol Biol Evol , vol.28 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5    Kumar, S.6
  • 23
    • 0030749810 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method
    • PID: 9214744, COI: 1:CAS:528:DyaK2sXksVahs7k%3D
    • Yang ZH, Rannala B (1997) Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol Biol Evol 14:717–724
    • (1997) Mol Biol Evol , vol.14 , pp. 717-724
    • Yang, Z.H.1    Rannala, B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.