StrainVis: interactive visual strain-level analysis of microbiome data

Background Microbiomes contain multiple conspecific strains whose genomic differences arise from both single nucleotide variants (SNVs) and structural variation (insertions, deletions, recombination). Recently, computational tools to assess strain-level differences became available, based either on average nucleotide identity (ANI) or on the average pairwise synteny (APSS) of strains, which are sensitive, respectively, to either SNVs or to structural variation. However, strain-level analyses remain technically challenging and fragmented across approaches and combining these complementary signals typically requires substantial bioinformatic expertise. Results Here we present StrainVis , a web-based analysis and visualization platform that integrates outputs from both ANI- and APSS-based strain tracking tools to enable unified, interactive exploration of within-species diversity. StrainVis allows users to perform per-species and multi-species comparisons, incorporate metadata and gene annotations, and generate statistical summaries and publication-ready figures without programming. Conclusions By lowering technical barriers and enabling joint interpretation of sequence and structural variation, StrainVis makes advanced strain-level microbiome analysis accessible to a broader community and facilitates discovery of evolutionary patterns that would be missed by single-method approaches alone.