Journal
MOLECULAR ECOLOGY RESOURCES
Volume 10, Issue 6, Pages 1085-1088Publisher
WILEY-BLACKWELL
DOI: 10.1111/j.1755-0998.2010.02862.x
Keywords
computer program; molecular evolution; population genetics; SNP
Funding
- National Outstanding Youth Science Foundation of China [30625016]
- National Science Foundation of China [30890034, 30971577]
- 863 Program [2007AA02Z312]
- Shanghai Leading Academic Discipline Project [B111]
- Center for Evolutionary Biology
- Science and Technology Commission of Shanghai Municipality [09ZR1436400]
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences [2008KIP311]
- SA-SIBS
- K.C.Wong Education Foundation, Hong Kong
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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 http://www.picb.ac.cn/similar to xushua/index.files/Download_PEAS.htm.
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