fastreeR

fastreeR calculates distances, builds phylogenetic trees, or performs hierarchical clustering between the samples of a VCF or FASTA file.

Key Features:

• Distance Calculation: Computes genetic distances between samples directly from VCF or FASTA files.
• Phylogenetic Tree Construction: Builds phylogenetic trees from calculated distances.
• Hierarchical Clustering: Performs hierarchical clustering between samples based on genetic variation.
• Java Implementation: Functions are implemented in Java-11 and called via rJava for computational efficiency.
• Parallel Processing: Parallel implementation operates directly on the VCF or FASTA file for fast execution.

Scientific Applications:

• Variant Analysis: Processes VCF files containing genetic variant data for population structure inference.
• Sequence Analysis: Analyzes FASTA files for phylogenetic relationships among samples.

Methodology:

Functions are implemented in Java-11 and called via rJava, with parallel implementation operating directly on VCF or FASTA files.