VCF2PopTree

VCF2PopTree constructs population phylogenies from genome-wide single nucleotide polymorphism (SNP) genotype data in Variant Call Format (VCF) to infer evolutionary relationships among populations.

Key Features:

• Input format: Parses genotype data in Variant Call Format (VCF).
• Data type: Operates on genome-wide single nucleotide polymorphisms (SNPs).
• Implementation: Implemented in JavaScript and executes client-side.
• Phylogenetic algorithms: Supports UPGMA (Unweighted Pair Group Method with Arithmetic Mean) and Neighbour-Joining.
• Outputs: Produces pairwise-diversity matrices in MEGA and PHYLIP formats and phylogenetic trees in Newick format.
• Performance: Capable of reading and analyzing a 1 GB VCF file within five minutes (as reported).

Scientific Applications:

• Population phylogenetics: Infers evolutionary relationships among populations using genome-wide SNP data.
• Population genetics analyses: Computes pairwise diversity metrics for comparative population genetic studies.
• Downstream phylogenetic integration: Provides MEGA, PHYLIP, and Newick outputs for use with other phylogenetic software.

Methodology:

Parses VCF genotype data, computes pairwise-diversity matrices, and constructs phylogenetic trees using UPGMA and Neighbour-Joining, exporting matrices in MEGA and PHYLIP formats and trees in Newick format.