SANS
SANS – Alignment-Free Phylogenetic Reconstruction
SANS is a freely available command-line tool for phylogenetic reconstruction from sequence data. It is alignment- and reference-free and accepts one or multiple FASTA or FASTQ files containing complete genomes, assembled contigs, or raw reads. SANS uses shared sequence segments, represented as k-mers, as indicators of phylogenetic splits. These splits are combined, weighted, filtered, and exported in tab-separated format, Newick, or Nexus format for downstream visualization.
Key benefits
Performs phylogenetic reconstruction without alignment or reference genomes
Accepts complete genomes, assembled contigs, or raw sequencing reads
Supports input in FASTA and FASTQ format
Generates phylogenetic splits based on shared k-mer patterns
Available as a C++ command-line tool and as a CloWM workflow
Applications
Alignment-free phylogenetic analysis of genome-scale data
Comparative analysis of complete genomes or assembled contigs
Phylogenetic reconstruction directly from raw reads
Generation of trees or networks for visualization in tools such as SplitsTree
Integration into automated workflows for large-scale sequence comparison
Intended use
SANS is intended for bioinformaticians, microbial genomicists, evolutionary biologists, and phylogenomics researchers who need alignment-free methods for reconstructing phylogenetic relationships from sequence data. It is particularly suited for users working with large genome datasets, draft assemblies, or raw reads where reference-based or alignment-based approaches may be impractical.
Contact:
Website