Small scripts for population genetics analysis.
Most of the scripts contain detailed usage in the codes.
By Zhuo CHEN, mail: chenomics@163.com or zhuochen@fafu.edu.cn
Calculate SNP allele frequency for selected groups of samples.
Add color annotation to samples in a nexus format tree. The colors are added to the branches.
Dissect the output Q file of ADMIXTURE population structure inference.
Transform eigenstart geno file to fasta sequence file.
Transform eigenstart geno file to fasta sequence file, with a pseudo reference sequence.
Transform hapmap format file to eigenstart geno file. May not adapt to all types of hapmap file.
Nucleotide diversity parameter Pi, with heterozygous genotype treated as an independent genotype.
Transform VCF file to group allele frequency table. Prepare input file for Treemix. TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations.
Transform VCF file to eigenstart geno format. Typically for ADMIXTURE inputs.
Pick SNPs from VCF file and transform to aligned fasta format sequences for selected samples. Commonly used for the construction of clustering trees.