Y-LineageTracker

Y-LineageTracker analyzes next-generation sequencing (NGS) data of the human Y chromosome to classify NRY haplogroups, genotype Y-STRs, construct phylogenies and haplotype networks, and estimate divergence times and TMRCA for paternal lineage studies.

Key Features:

• NGS Y-chromosome processing: Processes high-throughput NGS data targeted to the non-recombining region of the Y chromosome (NRY).
• Haplogroup classification and clustering: Classifies NRY haplogroups and clusters samples into specific paternal lineages.
• Phylogeny construction: Constructs phylogenetic trees to represent evolutionary relationships among haplogroups.
• Divergence time estimation: Estimates divergence times for haplogroups to provide temporal context for lineage evolution.
• Y-STR genotyping and statistics: Genotypes Y-STR loci and performs statistical calculations to quantify Y-STR variation.
• Y-STR network analysis: Builds networks depicting relationships among Y-STR haplotypes.
• TMRCA estimation: Estimates time to the most recent common ancestor (TMRCA) for Y-STR haplotypes.
• Visualization output: Produces publication-quality visualizations of haplogroups, phylogenies, and networks.

Scientific Applications:

• Paternal lineage tracing: Enables high-resolution reconstruction of paternal ancestry using NRY haplogroups and Y-STRs.
• Population genetics: Facilitates analysis of genetic diversity, population structure, and evolutionary history across populations.
• Anthropological and migration studies: Supports inference of human migration patterns and demographic changes through haplogroup and Y-STR analyses.

Methodology:

Integrates modular computational strategies to analyze NGS-derived Y-DNA (NRY and Y-STRs), supports multiple input formats, and produces publication-quality visualizations.