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PEAS V1.0: a package for elementary analysis of SNP data.

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Τίτλος: PEAS V1.0: a package for elementary analysis of SNP data.
Συγγραφείς: SHUHUA XU1,2 xushua@picb.ac.cn, GUPTA, SANCHIT1, LI JIN1,2,3,4 ljin007@gmail.com
Πηγή: Molecular Ecology Resources. Nov2010, Vol. 10 Issue 6, p1085-1088. 4p. 1 Chart.
Θεματικοί όροι: *Computer software, *Nucleotide sequence, *Genetics, *Molecular phylogeny, *Molecular evolution
Περίληψη: We have developed a software package named PEAS to facilitate analyses of large data sets of single nucleotide polymorphisms (SNPs) for population genetics and molecular phylogenetics studies. PEAS reads SNP data in various formats as input and is versatile in data formatting; using PEAS, it is easy to create input files for many popular packages, such as STRUCTURE, frappe, Arlequin, Haploview, LDhat, PLINK, EIGENSOFT, PHASE, fastPHASE, MEGA and PHYLIP. In addition, PEAS fills up several analysis gaps in currently available computer programs in population genetics and molecular phylogenetics. Notably, (i) It calculates genetic distance matrices with bootstrapping for both individuals and populations from genome-wide high-density SNP data, and the output can be streamlined to MEGA and PHYLIP programs for further processing; (ii) It calculates genetic distances from STRUCTURE output and generates MEGA file to reconstruct component trees; (iii) It provides tools to conduct haplotype sharing analysis for phylogenetic studies based on high-density SNP data. To our knowledge, these analyses are not available in any other computer program. PEAS for Windows is freely available for academic users from . [ABSTRACT FROM AUTHOR]
Βάση Δεδομένων: Academic Search Index
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  Data: PEAS V1.0: a package for elementary analysis of SNP data.
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  Data: <searchLink fieldCode="AR" term="%22SHUHUA+XU%22">SHUHUA XU</searchLink><relatesTo>1,2</relatesTo><i> xushua@picb.ac.cn</i><br /><searchLink fieldCode="AR" term="%22GUPTA%2C+SANCHIT%22">GUPTA, SANCHIT</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22LI+JIN%22">LI JIN</searchLink><relatesTo>1,2,3,4</relatesTo><i> ljin007@gmail.com</i>
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  Data: <searchLink fieldCode="JN" term="%22Molecular+Ecology+Resources%22">Molecular Ecology Resources</searchLink>. Nov2010, Vol. 10 Issue 6, p1085-1088. 4p. 1 Chart.
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  Data: *<searchLink fieldCode="DE" term="%22Computer+software%22">Computer software</searchLink><br />*<searchLink fieldCode="DE" term="%22Nucleotide+sequence%22">Nucleotide sequence</searchLink><br />*<searchLink fieldCode="DE" term="%22Genetics%22">Genetics</searchLink><br />*<searchLink fieldCode="DE" term="%22Molecular+phylogeny%22">Molecular phylogeny</searchLink><br />*<searchLink fieldCode="DE" term="%22Molecular+evolution%22">Molecular evolution</searchLink>
– Name: Abstract
  Label: Abstract
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  Data: We have developed a software package named PEAS to facilitate analyses of large data sets of single nucleotide polymorphisms (SNPs) for population genetics and molecular phylogenetics studies. PEAS reads SNP data in various formats as input and is versatile in data formatting; using PEAS, it is easy to create input files for many popular packages, such as STRUCTURE, frappe, Arlequin, Haploview, LDhat, PLINK, EIGENSOFT, PHASE, fastPHASE, MEGA and PHYLIP. In addition, PEAS fills up several analysis gaps in currently available computer programs in population genetics and molecular phylogenetics. Notably, (i) It calculates genetic distance matrices with bootstrapping for both individuals and populations from genome-wide high-density SNP data, and the output can be streamlined to MEGA and PHYLIP programs for further processing; (ii) It calculates genetic distances from STRUCTURE output and generates MEGA file to reconstruct component trees; (iii) It provides tools to conduct haplotype sharing analysis for phylogenetic studies based on high-density SNP data. To our knowledge, these analyses are not available in any other computer program. PEAS for Windows is freely available for academic users from . [ABSTRACT FROM AUTHOR]
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        Value: 10.1111/j.1755-0998.2010.02862.x
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        Text: English
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      – SubjectFull: Nucleotide sequence
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      – SubjectFull: Genetics
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      – SubjectFull: Molecular phylogeny
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      – SubjectFull: Molecular evolution
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      – TitleFull: PEAS V1.0: a package for elementary analysis of SNP data.
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            NameFull: SHUHUA XU
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              M: 11
              Text: Nov2010
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              Y: 2010
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