메뉴 건너뛰기




Volumn 2009, Issue 5, 2009, Pages 91-95

PhyLIS: A simple GNU/Linux distribution for phlogenetics and phyloinformatics

Author keywords

Linux; Operating system; Phylogenetics; Phyloinformatics

Indexed keywords

ARTICLE; AUTOMATION; BIOINFORMATICS; COMPUTER PROGRAM; INFORMATION SYSTEM; MOLECULAR EVOLUTION; PHYLOGENY;

EID: 70349286819     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (5)

References (37)
  • 1
    • 32044455956 scopus 로고    scopus 로고
    • The tree of life and the grand synthesis of biology
    • Cracraft J, Donoghue MJ, eds, New York: Oxford University Press;
    • Hillis DM. The tree of life and the grand synthesis of biology. In: Cracraft J, Donoghue MJ, eds. Assembling the tree of life. New York: Oxford University Press; 2004:545-7.
    • (2004) Assembling the tree of life , pp. 545-547
    • Hillis, D.M.1
  • 2
    • 70349288775 scopus 로고    scopus 로고
    • NERC Environmental Bioinformatics Centre. Bio-Linux. Version 5.0.2009; Available from
    • NERC Environmental Bioinformatics Centre. Bio-Linux. Version 5.0.2009; Available from http://nebc.nox.ac.uk/tools/bio-linux.
  • 3
    • 70349274838 scopus 로고    scopus 로고
    • Anjar U. Scibuntu: Ubuntu Linux for scientists. Version 0.4-beta. 2006; Available from
    • Anjar U. Scibuntu: Ubuntu Linux for scientists. Version 0.4-beta. 2006; Available from http://scibunta.sourceforge.net/index.html.
  • 4
    • 34548575126 scopus 로고    scopus 로고
    • Species trees from gene trees: Reconstructing bayesian posterior distributions of a species phylogeny using estimated gene tree distributions
    • Liu L, Pearl DK. Species trees from gene trees: Reconstructing bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst Biol. 2001;56:504-14.
    • (2001) Syst Biol , vol.56 , pp. 504-514
    • Liu, L.1    Pearl, D.K.2
  • 5
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003; 19:1572-4.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 6
    • 33750403801 scopus 로고    scopus 로고
    • Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis A. RAxML-VI-HPC; Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22:2688.
    • (2006) Bioinformatics , vol.22 , pp. 2688
    • Stamatakis, A.1
  • 7
  • 8
    • 1042304216 scopus 로고    scopus 로고
    • Paradis E, Claude J, Strimmer K. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics. 2004;20:289-90.
    • Paradis E, Claude J, Strimmer K. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics. 2004;20:289-90.
  • 9
    • 32144453296 scopus 로고    scopus 로고
    • apTreeshape: Statistical analysis of phylogenetic tree shape
    • Bortolussi N, Durand E, Blum M, Francois O. apTreeshape: statistical analysis of phylogenetic tree shape. Bioinformatics. 2006; 22:363-4.
    • (2006) Bioinformatics , vol.22 , pp. 363-364
    • Bortolussi, N.1    Durand, E.2    Blum, M.3    Francois, O.4
  • 10
    • 38649110663 scopus 로고    scopus 로고
    • Bayesian evolutionary analysis by sampling trees
    • Drummond AJ, Rambaut A. BEAST. Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007;7:214-22.
    • (2007) BMC Evol Biol , vol.7 , pp. 214-222
    • Drummond, A.J.1    Rambaut, A.2    BEAST3
  • 11
    • 18644368714 scopus 로고    scopus 로고
    • The Bioperl toolkit: Pert modules for the life sciences
    • Stajich J, Block D, Boulez K, et al. The Bioperl toolkit: Pert modules for the life sciences. Genome Res. 2002; 12:1611-8.
    • (2002) Genome Res , vol.12 , pp. 1611-1618
    • Stajich, J.1    Block, D.2    Boulez, K.3
  • 12
    • 0345276226 scopus 로고    scopus 로고
    • Biopython: Python tools for computational biology
    • Chapman B, Chang J. Biopython: Python tools for computational biology. ACM SIGBIO Newsletter. 2000;20:15-9.
    • (2000) ACM SIGBIO Newsletter , vol.20 , pp. 15-19
    • Chapman, B.1    Chang, J.2
  • 13
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul S, Madden T, Schaffer A, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389-402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.1    Madden, T.2    Schaffer, A.3
  • 14
    • 33846839390 scopus 로고    scopus 로고
    • Bayesian estimation of concordance among gene trees
    • Ane C, Larget B, Baum D, Smith S, Rokas A. Bayesian estimation of concordance among gene trees. Mol Biol Evol. 2007;24:412-26.
    • (2007) Mol Biol Evol , vol.24 , pp. 412-426
    • Ane, C.1    Larget, B.2    Baum, D.3    Smith, S.4    Rokas, A.5
  • 15
    • 0042121237 scopus 로고    scopus 로고
    • Multiple sequence alignment with the Clustal series of programs
    • Chenna R, Sugawara H, Koike T, et al. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 2003;31:3497-500.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3497-3500
    • Chenna, R.1    Sugawara, H.2    Koike, T.3
  • 16
    • 0032945593 scopus 로고    scopus 로고
    • DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment
    • Morgenstern B. DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics. 1999; 15:211-8.
    • (1999) Bioinformatics , vol.15 , pp. 211-218
    • Morgenstern, B.1
  • 17
    • 70349299498 scopus 로고    scopus 로고
    • Available from
    • Available from http://beast.bio.ed.ac.uk/.
  • 20
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy SR. Profile hidden Markov models. Bioinformatics. 1998;14:755-63.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 21
    • 45849154165 scopus 로고    scopus 로고
    • jModel Test: Phylogenetic model averaging
    • Posada D. jModel Test: Phylogenetic model averaging. Mol Biol Evol. 2008;25:1253-6.
    • (2008) Mol Biol Evol , vol.25 , pp. 1253-1256
    • Posada, D.1
  • 22
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059-66.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 23
    • 70349279590 scopus 로고    scopus 로고
    • Maddison W, Maddison D. Mesquite: a modular system for evolutionary analysis. Version 2.6. 2009; Available from
    • Maddison W, Maddison D. Mesquite: a modular system for evolutionary analysis. Version 2.6. 2009; Available from http://mesquiteproject.org.
  • 24
    • 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
  • 25
    • 11944264347 scopus 로고    scopus 로고
    • Phylogenetic comparative analysis: A modeling approach for adaptive evolution
    • Butler MA, King AA. Phylogenetic comparative analysis: A modeling approach for adaptive evolution. Am Nat. 2004; 164:683-95.
    • (2004) Am Nat , vol.164 , pp. 683-695
    • Butler, M.A.1    King, A.A.2
  • 26
    • 33645801601 scopus 로고    scopus 로고
    • Paloverde: On OpenGL 3D phylogeny browser
    • Sanderson MJ. Paloverde: on OpenGL 3D phylogeny browser. Bioinformatics. 2006;22:1004-6.
    • (2006) Bioinformatics , vol.22 , pp. 1004-1006
    • Sanderson, M.J.1
  • 27
    • 70349270282 scopus 로고    scopus 로고
    • Felsenstein J. PHYLIP phylogeny inference package, Version 3.68. 2009; Available from
    • Felsenstein J. PHYLIP (phylogeny inference package). Version 3.68. 2009; Available from http://evolution.genetics.washington.edu/phylip.html.
  • 28
    • 51749095104 scopus 로고    scopus 로고
    • Phylocom: Software for the analysis of phylogenetic community structure and trait evolution
    • Webb C, Ackerly D, Kembel S. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics. 2008;24:2098-100.
    • (2008) Bioinformatics , vol.24 , pp. 2098-2100
    • Webb, C.1    Ackerly, D.2    Kembel, S.3
  • 29
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52:696-704.
    • (2003) Syst Biol , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 30
    • 70349285640 scopus 로고    scopus 로고
    • Weir J, Schlutter D. PhySim: phylogenetic tree simulation package. Version 1.0. 2007; Available from
    • Weir J, Schlutter D. PhySim: phylogenetic tree simulation package. Version 1.0. 2007; Available from http://cran.r-project.org/web/packages/ PhySim/index.html.
  • 31
    • 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
  • 32
    • 3543097981 scopus 로고    scopus 로고
    • Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
    • Grasso C, Lee C. Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems. Bioinformatics. 2004;20:1546-56.
    • (2004) Bioinformatics , vol.20 , pp. 1546-1556
    • Grasso, C.1    Lee, C.2
  • 33
    • 85142133654 scopus 로고    scopus 로고
    • Sanderson MJ. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics. 2003 2003;19:301-2.
    • Sanderson MJ. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics. 2003 2003;19:301-2.
  • 34
    • 70349281091 scopus 로고    scopus 로고
    • Gilbert D. Readseq. Version 2.2001; Available from
    • Gilbert D. Readseq. Version 2.2001; Available from http://ubio.bio.indiana.edu/soft/molbio/readseq/java/.
  • 35
    • 0030464460 scopus 로고    scopus 로고
    • SEAVIEW and PHYLO_WN: Two graphic tools for sequence alignment and molecular phylogeny
    • Galtier N, Gouy M, Gautier C. SEAVIEW and PHYLO_WN: two graphic tools for sequence alignment and molecular phylogeny. Bioinformatics. 1996;12:543-8.
    • (1996) Bioinformatics , vol.12 , pp. 543-548
    • Galtier, N.1    Gouy, M.2    Gautier, C.3
  • 36
    • 0030928378 scopus 로고    scopus 로고
    • Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along pbylogenetic trees
    • Rambaut A, Grass NC. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along pbylogenetic trees. Bioinformatics. 1997;13:235-8.
    • (1997) Bioinformatics , vol.13 , pp. 235-238
    • Rambaut, A.1    Grass, N.C.2
  • 37
    • 0034623005 scopus 로고    scopus 로고
    • A novel method for fast and accurate multiple sequence alignment
    • Notredame C, Higgins DG, Heringa, J. T-coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000;302:205-17.
    • (2000) J Mol Biol , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa3    T-coffee, J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.