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Volumn 13, Issue , 2012, Pages

EggLib: Processing, analysis and simulation tools for population genetics and genomics

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; EVOLUTIONARY GENETICS AND GENOMICS LIBRARY; GENE LIBRARY; GENETIC ANALYSIS; GENOMICS; NUCLEOTIDE SEQUENCE; POPULATION GENETICS; SIMULATION; COMPUTER SIMULATION;

EID: 84859499806     PISSN: None     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/1471-2156-13-27     Document Type: Article
Times cited : (105)

References (31)
  • 1
    • 37749031255 scopus 로고    scopus 로고
    • Next-generation sequencing transforms today's biology
    • 10.1038/nmeth1156, 18165802
    • Schuster S. Next-generation sequencing transforms today's biology. Nat Methods 2008, 5:16-18. 10.1038/nmeth1156, 18165802.
    • (2008) Nat Methods , vol.5 , pp. 16-18
    • Schuster, S.1
  • 5
    • 36948999784 scopus 로고    scopus 로고
    • A primer on Python for life science researchers
    • Bassi S. A primer on Python for life science researchers. PLoS Comput Biol 2007, 3:2052-2057.
    • (2007) PLoS Comput Biol , vol.3 , pp. 2052-2057
    • Bassi, S.1
  • 8
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • 10.1093/nar/gkh340, 390337, 15034147
    • Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 10
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • 10.1093/molbev/msm088, 17483113
    • Yang ZH. PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 2007, 24:1586-1591. 10.1093/molbev/msm088, 17483113.
    • (2007) Mol Biol Evol , vol.24 , pp. 1586-1591
    • Yang, Z.H.1
  • 11
    • 78149388939 scopus 로고    scopus 로고
    • Approximate Bayesian computation in evolution and ecology
    • Beaumont MA. Approximate Bayesian computation in evolution and ecology. Annu Rev Ecol Evol Syst 2010, 41:379-406.
    • (2010) Annu Rev Ecol Evol Syst , vol.41 , pp. 379-406
    • Beaumont, M.A.1
  • 12
    • 0036964474 scopus 로고    scopus 로고
    • Approximate Bayesian computation in population genetics
    • 1462356, 12524368
    • Beaumont MA, Zhang W, Balding DJ. Approximate Bayesian computation in population genetics. Genetics 2002, 162:2025-2035. 1462356, 12524368.
    • (2002) Genetics , vol.162 , pp. 2025-2035
    • Beaumont, M.A.1    Zhang, W.2    Balding, D.J.3
  • 13
    • 33748799967 scopus 로고    scopus 로고
    • Modern computational approaches for analysis molecular genetics variation data
    • Marjoram P, Tavaré S. Modern computational approaches for analysis molecular genetics variation data. Nat Rev Genet 2006, 7:759-770.
    • (2006) Nat Rev Genet , vol.7 , pp. 759-770
    • Marjoram, P.1    Tavaré, S.2
  • 16
    • 84860887891 scopus 로고    scopus 로고
    • Sphinx: Python documentation generation
    • Sphinx: Python documentation generation. , http://sphinx.pocoo.org/
  • 18
    • 33745955637 scopus 로고    scopus 로고
    • Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics
    • 10.1186/1471-2105-7-188, 1501049, 16594991
    • Dutheil J, Gaillard S, Bazin E, Glémin S, Ranwez V, Galtier N, Belkhir K. Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. BMC Bioinformatics 2006, 7:188. 10.1186/1471-2105-7-188, 1501049, 16594991.
    • (2006) BMC Bioinformatics , vol.7 , pp. 188
    • Dutheil, J.1    Gaillard, S.2    Bazin, E.3    Glémin, S.4    Ranwez, V.5    Galtier, N.6    Belkhir, K.7
  • 19
    • 0347513220 scopus 로고    scopus 로고
    • DnaSP, DNA polymorphism analyses by the coalescent and other methods
    • 10.1093/bioinformatics/btg359, 14668244
    • Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 2003, 19:2496-2497. 10.1093/bioinformatics/btg359, 14668244.
    • (2003) Bioinformatics , vol.19 , pp. 2496-2497
    • Rozas, J.1    Sanchez-DelBarrio, J.C.2    Messeguer, X.3    Rozas, R.4
  • 20
    • 0036184745 scopus 로고    scopus 로고
    • Generating samples under a Wright-Fisher neutral model of genetic variation
    • 10.1093/bioinformatics/18.2.337, 11847089
    • Hudson RR. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 2002, 18:337-338. 10.1093/bioinformatics/18.2.337, 11847089.
    • (2002) Bioinformatics , vol.18 , pp. 337-338
    • Hudson, R.R.1
  • 21
  • 22
    • 56649113038 scopus 로고    scopus 로고
    • Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation
    • 10.1093/bioinformatics/btn514, 2639274, 18842597
    • Cornuet JM, Santos F, Beaumont MA, Robert CP, Marin JM, Balding DJ, Guillemaud T, Estoup A. Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation. Bioinformatics 2008, 24:2713-2719. 10.1093/bioinformatics/btn514, 2639274, 18842597.
    • (2008) Bioinformatics , vol.24 , pp. 2713-2719
    • Cornuet, J.M.1    Santos, F.2    Beaumont, M.A.3    Robert, C.P.4    Marin, J.M.5    Balding, D.J.6    Guillemaud, T.7    Estoup, A.8
  • 23
    • 77951177432 scopus 로고    scopus 로고
    • ABCtoolbox: a versatile toolkit for approximate Bayesian computations
    • 10.1186/1471-2105-11-116, 2848233, 20202215
    • Wegmann D, Leuenberger C, Neuenschwander S, Excoffier L. ABCtoolbox: a versatile toolkit for approximate Bayesian computations. BMC Bioinformatics 2010, 11:116. 10.1186/1471-2105-11-116, 2848233, 20202215.
    • (2010) BMC Bioinformatics , vol.11 , pp. 116
    • Wegmann, D.1    Leuenberger, C.2    Neuenschwander, S.3    Excoffier, L.4
  • 24
    • 77954714407 scopus 로고    scopus 로고
    • MsABC: a modification of Hudson's ms to facilitate multi-locus ABC analysis
    • 10.1111/j.1755-0998.2010.02832.x, 21565078
    • Pavlidis P, Laurent S, Stephan W. msABC: a modification of Hudson's ms to facilitate multi-locus ABC analysis. Mol Ecol Resour 2010, 10:723-727. 10.1111/j.1755-0998.2010.02832.x, 21565078.
    • (2010) Mol Ecol Resour , vol.10 , pp. 723-727
    • Pavlidis, P.1    Laurent, S.2    Stephan, W.3
  • 25
    • 67749135914 scopus 로고    scopus 로고
    • Automating approximate Bayesian computation by local linear regression
    • 2712468, 19583871
    • Thornton KR. Automating approximate Bayesian computation by local linear regression. BMC Genet 2009, 10:35. 2712468, 19583871.
    • (2009) BMC Genet , vol.10 , pp. 35
    • Thornton, K.R.1
  • 26
    • 0344464730 scopus 로고    scopus 로고
    • Libsequence: a C++ class library for evolution genetic analysis
    • Thornton K. Libsequence: a C++ class library for evolution genetic analysis. Bioinformatics 2003, 22:2325-2327.
    • (2003) Bioinformatics , vol.22 , pp. 2325-2327
    • Thornton, K.1
  • 27
    • 80051669931 scopus 로고    scopus 로고
    • Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems
    • 10.1111/j.1365-294X.2011.05189.x, 21777317
    • St Onge KR, Källman T, Slotte T, Lascoux M, Palmé AE. Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems. Mol Ecol 2011, 20:3306-3320. 10.1111/j.1365-294X.2011.05189.x, 21777317.
    • (2011) Mol Ecol , vol.20 , pp. 3306-3320
    • St. Onge, K.R.1    Källman, T.2    Slotte, T.3    Lascoux, M.4    Palmé, A.E.5
  • 28
    • 77951582540 scopus 로고    scopus 로고
    • Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci
    • 10.1093/molbev/msp301, 20031927
    • Li Y, Stocks M, Hemmila S, Källman T, Zhu H, Zhou Y, Chen J, Liu J, Lascoux M. Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci. Mol Biol Evol 2010, 27:1001-1014. 10.1093/molbev/msp301, 20031927.
    • (2010) Mol Biol Evol , vol.27 , pp. 1001-1014
    • Li, Y.1    Stocks, M.2    Hemmila, S.3    Källman, T.4    Zhu, H.5    Zhou, Y.6    Chen, J.7    Liu, J.8    Lascoux, M.9
  • 29
    • 78650003883 scopus 로고    scopus 로고
    • The Pleistocene demography of an alpine juniper of the Qinghai-Tibetan Plateau: tabula rasa, cryptic refugia or something else?
    • Li ZH, Zhang QA, Liu JQ, Källman T, Lascoux M. The Pleistocene demography of an alpine juniper of the Qinghai-Tibetan Plateau: tabula rasa, cryptic refugia or something else?. J Biogeogr 2011, 38:31-43.
    • (2011) J Biogeogr , vol.38 , pp. 31-43
    • Li, Z.H.1    Zhang, Q.A.2    Liu, J.Q.3    Källman, T.4    Lascoux, M.5
  • 30
    • 79960857055 scopus 로고    scopus 로고
    • Molecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume Medicago truncatula
    • 10.1186/1471-2148-11-229, 3199773, 21806823
    • De Mita S, Chantret N, Loridon K, Ronfort J, Bataillon T. Molecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume Medicago truncatula. BMC Evol Biol 2011, 11:229. 10.1186/1471-2148-11-229, 3199773, 21806823.
    • (2011) BMC Evol Biol , vol.11 , pp. 229
    • De Mita, S.1    Chantret, N.2    Loridon, K.3    Ronfort, J.4    Bataillon, T.5
  • 31
    • 79955568693 scopus 로고    scopus 로고
    • SNiPlay: a web-based tool for detection, management and analysis of SNPs, Application to grapevine diversity projects
    • 10.1186/1471-2105-12-134, 3102043, 21545712
    • Dereeper A, Nicolas S, Le Cunff L, Bacilieri R, Doligez A, Peros JP, Ruiz M, This P. SNiPlay: a web-based tool for detection, management and analysis of SNPs, Application to grapevine diversity projects. BMC Bioinformatics 2011, 12:134. 10.1186/1471-2105-12-134, 3102043, 21545712.
    • (2011) BMC Bioinformatics , vol.12 , pp. 134
    • Dereeper, A.1    Nicolas, S.2    Le Cunff, L.3    Bacilieri, R.4    Doligez, A.5    Peros, J.P.6    Ruiz, M.7    This, P.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.