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shengxinzhuan / vcfpop

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vcfpop

Performing population genetics analyses based on NGS data for haploids, diploids, autopolyploids and aneuploids.

The functions of VCFPOP consist of:

  1. Variant information, individual, genotype and locus filters;
  2. Haplotype extraction from phased genotypes;
  3. File format conversion;
  4. Genetic diversity index estimation and genotypic equilibrium test;
  5. Individual statistics estimation (inbreeding coefficient, kinship coefficient, heterozygosity);
  6. Genetic differentiation index estimation and test;
  7. Genetic distance estimation;
  8. Analysis of molecular variances;
  9. Population assignment;
  10. Relatedness coefficient estimation;
  11. Kinship coefficient estimation;
  12. Principal coordinate analysis;
  13. Hierarchical clustering;
  14. Bayesian clustering.

v 1.05 x64 executables (for Windows, Ubuntu and Mac OS X), user manual, source code and example files https://github.com/huangkang1987/vcfpop/blob/master/archive/vcfpop%20v1.05.zip?raw=true

Bug report and suggestions huangkang@nwu.edu.cn

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License:GNU General Public License v3.0

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