SANS

SANS reconstructs phylogenetic relationships from complete genomes, assembled contigs, or raw reads in FASTA/FASTQ formats using alignment- and reference-free k-mer analysis and colored de Bruijn graphs.

Key Features:

• Alignment- and reference-free: Infers phylogenetic signals without multiple sequence alignment or reliance on a reference genome.
• Input formats: Accepts complete genomes, assembled contigs, and raw reads in FASTA and FASTQ files.
• K-mer based split identification: Leverages k-mers (short sequence segments) shared among genomes to identify phylogenetic splits.
• Colored de Bruijn graph construction: Constructs a colored de Bruijn graph from input genomic data to extract common subsequences across samples.
• Split processing: Combines, weights, and filters inferred splits to produce final phylogenetic signals.
• Output formats: Exports results in tab-separated values and Newick format.
• Visualization compatibility: Outputs are compatible with tree and network visualization tools such as SplitsTree.
• Implementation and performance: Implemented in C++ to provide computational efficiency for large datasets.
• Scale and accuracy: Demonstrated suitability for large-scale phylogenomic studies with comparable or superior accuracy and efficiency relative to existing whole-genome methods.

Scientific Applications:

• Large-scale comparative phylogenomics: Enables phylogenetic analysis of many genomes when close references are unavailable or assemblies are incomplete.
• Phylogeny from raw reads: Allows inference of evolutionary relationships directly from FASTQ raw read data without assembly.
• Analysis of draft or partial assemblies: Supports phylogenetic inference using assembled contigs from incomplete genomes.
• Tree and network reconstruction: Produces splits and Newick outputs for downstream tree or network visualization and comparative analyses.

Methodology:

Processes complete genomes, assembled contigs, or raw FASTA/FASTQ reads to construct a colored de Bruijn graph, leverages k-mers to identify phylogenetic splits, combines, weights, and filters those splits, and outputs results in tab-separated or Newick format; implemented in C++.