Minimizer Sampling & Collinear DP Chaining
High-throughput long-read alignment indexing using (w, k)-minimizers. Explore sliding hash windows, 2D anchor dot-plot matching, and dynamic programming collinear chaining.
Interactive Visualizers & Concepts
Algorithms
Interactive explorations of fundamental computational biology algorithms — from long-read minimizer chaining and FM-index exact matching to Wheeler graph pangenomics and sequence alignment.
FM-Index & BWT Backward Search
Burrows-Wheeler Transform with Last-to-First (LF) mapping and occurrence counting for sub-linear query matching across gigabase reference genomes.
Wheeler Graph Ordering & Recognition (Wheelie)
Algorithms for recognizing and sorting Wheeler graph topologies, generalizing BWT-style index search to pangenomic reference variation graphs.
Needleman-Wunsch & Smith-Waterman Alignment
Exact 2D dynamic programming pairwise sequence alignment supporting global (Needleman-Wunsch), local (Smith-Waterman), and Gotoh affine gap penalties.
CLI Command:
align ACGTAGCTA ACGTCGCTAWavefront Alignment Algorithm (WFA)
Exact gap-affine pairwise alignment running in O(s · d) time. Explore diagonal wavefront frontier expansion, free Longest Common Prefix (LCP) extensions, and matrix pruning.
CLI Command:
wfa ACGTAGCTA ACGTCGCTADe Bruijn Graph (Eulerian Path Genome Assembly)
Deconstruct sequencing reads into (k-1)-mer nodes and directed k-mer edges. Explore O(E) Eulerian path assembly, tip clipping, bubble popping, and unitig compaction.
CLI Command:
debruijn TAATGCCATGGGATGTTString Graphs & Overlap-Layout-Consensus (OLC)
Long-read exact prefix-suffix overlap graphs without k-mer chopping. Explore Myers’ O(V+E) transitive reduction, contained read pruning, and read tiling layout.
CLI Command:
stringgraphProfile Hidden Markov Models (pHMMs)
Model conserved biological domains and sequence families with insertion/deletion tolerance. Explore Viterbi optimal decoding, Forward-Backward posteriors, and Plan 7 topology.
CLI Command:
phmm TATAAAGeneralized Hidden Markov Models (GHMMs)
Predict exon-intron structures, splice junctions, and protein-coding CDS using explicit duration distributions f(d) and semi-Markov dynamic programming (GENSCAN / AUGUSTUS).
CLI Command:
geneDeep Learning Splice-Site Recognition (Splam / OpenSpliceAI)
Ultra-fast residual convolutional neural networks scoring donor (GT) and acceptor (AG) pre-mRNA junctions to filter spurious spliced transcript alignments.
CLI Command:
splam -hNo algorithms match your filter or search query.