AFnetwork

AFnetwork constructs alignment-free phylogenetic networks from whole-genome sequences to infer microbial evolutionary relationships while capturing recombination, lateral genetic transfer, and genome rearrangement in bacteria and archaea.

Key Features:

• Alignment-Free Approach: Infers phylogenetic relationships without multiple sequence alignment, avoiding MSA assumptions and alignment-induced biases.
• k-mer Based Analysis: Quantifies genomic similarity by analyzing the distribution and frequency of k-mers and counting shared k-mers among genomes, including an example dataset of 143 bacterial and archaeal genomes.
• Scalability: Implements computational procedures intended to handle large numbers of genomes and large datasets.
• Network Representation: Produces phylogenetic networks that represent both treelike and non-treelike (reticulate) evolutionary features.

Scientific Applications:

• Microbial Evolution Studies: Captures treelike and reticulate evolutionary events relevant to bacterial and archaeal evolution.
• Genomic Research: Enables analysis of whole-genome sequences to assess overall genomic relatedness without targeting specific loci.
• Evolutionary Biology: Facilitates exploration of processes such as recombination, lateral genetic transfer, and genome rearrangement that are poorly represented by tree models.

Methodology:

AFnetwork analyzes the distribution and frequency of k-mers across genomes, counts shared k-mers among genomes (e.g., 143 bacterial and archaeal genomes), and constructs a phylogenetic network that reflects both treelike and non-treelike relationships without requiring sequence alignment.