Implements methods for the analysis of pooled sequencing data generation. Syzygy is a variant calling method allowing: (i) single nucleotide polymorphism (SNP) calling on pooled data, (ii) estimation of allele frequencies of discovered variants, (iii) application of single-marker association test in pooled setting, (iv) group wise testing of rare and low frequency variants discovered, (v) power evaluation and quality control (QC) summary, as well as (vi) annotation of variants discovered in regions from primary sequencing data in BAM/SAM format.
Allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences. A toolbox specifically designed for the population genetic analysis of sequence data from pooled individuals.
Estimates evolutionary parameters from pooled next-generation sequencing single-nucleotide polymorphism data. The user submits a FASTA reference sequence(s), a Gene Transfer Format (.GTF) file with CDS information and a SNP report(s) in an increasing selection of formats. The program estimates nucleotide diversity, distance from the reference and gene diversity. Sites are flagged for multiple overlapping reading frames, and are categorized by polymorphism type: nonsynonymous, synonymous, or ambiguous. The results allow single nucleotide, single codon, sliding window, whole gene and whole genome/population analyses that aid in the detection of positive and purifying natural selection in the source population.