Performing population genetics analyses based on NGS data for haploids, diploids, autopolyploids and aneuploids.
The functions of VCFPOP consist of:
- Variant information, individual, genotype and locus filters;
- Haplotype extraction from phased genotypes;
- File format conversion;
- Genetic diversity index estimation and genotypic equilibrium test;
- Individual statistics estimation (inbreeding coefficient, kinship coefficient, heterozygosity);
- Genetic differentiation index estimation and test;
- Genetic distance estimation;
- Analysis of molecular variances;
- Population assignment;
- Relatedness coefficient estimation;
- Kinship coefficient estimation;
- Principal coordinate analysis;
- Hierarchical clustering;
- 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