EPIK

EPIK performs alignment-free phylogenetic placement of query DNA sequences onto an existing reference tree using informative phylo-k-mers to enable scalable placement of large numbers of queries (hundreds of thousands to millions).

Key Features:

• Alignment-free placement: Performs phylogenetic placement without requiring sequence alignment or de novo tree inference.
• Phylo-k-mers: Uses k-mers (phylo-k-mers) derived from DNA sequences as informative markers for placement relative to reference sequences.
• Mutual information filtering: Applies mutual information–based filtering to select the most informative phylo-k-mers, reducing computational load while maintaining placement precision.
• IPK integration: Integrates with IPK (Informative Phylo-K-mer) to compute and filter phylo-k-mers into filtered phylo-k-mer databases.
• Scalability: Designed for high-throughput placement of hundreds of thousands to millions of queries using filtered phylo-k-mer databases.
• Implementation: Implemented in C++ and Python.

Scientific Applications:

• Placement of newly sequenced DNA: Assigns newly sequenced DNA to positions within an existing high-quality reference tree.
• Large-scale evolutionary analysis: Enables large-scale phylogenetic studies that require rapid assignment of many query sequences.
• Genomics and evolutionary biology: Supports genomic and evolutionary-biology analyses that depend on scalable, precise phylogenetic placement.

Methodology:

Computes phylo-k-mers from reference data, filters phylo-k-mers using mutual information via IPK, and performs alignment-free placement of queries onto a reference tree using the resulting filtered phylo-k-mer databases while avoiding sequence alignment and de novo tree inference.