HaploGrep

HaploGrep classifies mitochondrial DNA (mtDNA) profiles into phylogenetic haplogroups to support evolutionary, forensic, and medical genetics analyses.

Key Features:

• Automated haplogroup classification: Performs automated assignment of mtDNA profiles to phylogenetic haplogroups based on a comprehensive reference tree.
• Rule-based quality control system: Applies a generic rule-based QC to identify artificial recombinants, detect missing variants, and annotate rare or phantom mutations.
• Support for high-throughput data: Accepts Variant Call Format (VCF) files for direct processing of large-scale mtDNA datasets.
• Graphical report generation: Produces graphical outputs including multiple sequence alignment formats, VCF outputs, and extended haplogroup QC reports.
• Phylogenetic tree generation: Generates a phylogenetic tree for input samples encoded relative to the revised Cambridge Reference Sequence (rCRS).
• Enhanced accuracy and speed: Incorporates new distance measures and algorithmic optimizations to improve classification accuracy and processing speed.

Scientific Applications:

• Evolutionary genetics: Enables analysis of mtDNA haplogroups to study human migration patterns and ancestral lineages.
• Forensic science: Supports haplogroup determination for identification of individuals or population inference from genetic evidence.
• Medical genetics: Facilitates investigation of associations between mtDNA haplogroups and disease predispositions linked to mitochondrial variation.

Methodology:

Uses a comprehensive phylogenetic tree summarizing published mtDNA sequences for automated haplogroup classification, applies a rule-based QC system, supports VCF input, generates a phylogenetic tree encoded relative to the revised Cambridge Reference Sequence, and employs new distance measures and algorithmic optimizations.