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PanAbyss is a tool for exploring and visualizing pangenome graphs. It allows users to search for and display regions of a pangenome using coordinates on a reference individual or based on annotations. It also enables searching for regions associated with a selected set of individuals (for example, those linked to a phenotype), computing proximity trees, and retrieving sequences from a given region.

Local Python sequence utilities for nucleotide composition, DNA and RNA reverse complements, NCBI genetic-code translation, six-frame candidate ORF enumeration, and IUPAC motif searches. Computase accepts raw nucleotide strings or one FASTA record and returns structured, bounded results with explicit scientific conventions.

PseudoScope is an automated, locally-executable computational pipeline designed specifically for comprehensive Pseudomonas aeruginosa genomic surveillance. It integrates seven essential analysis modules into a single, cohesive workflow: FASTA QC (assembly quality metrics), MLST (Oxford scheme), PAST serotyping (O-antigen typing), AMRFinderPlus (antimicrobial resistance gene detection), ABRicate (multi-database screening for resistance, virulence, plasmids, biocides), Ultimate Reporter (gene-centric integration with interactive HTML), and Visualisation Dashboard (publication-ready interactive plots including PCA, networks, boxplots). PseudoScope runs entirely locally (or on HPC clusters), protects data privacy, and produces beautiful interactive reports in minutes.

Kleboscope is an automated, locally‑executable computational pipeline designed specifically for comprehensive Klebsiella pneumoniae genomic surveillance. It addresses the growing threat of multidrug‑resistant and hypervirulent K. pneumoniae by integrating eight essential analysis modules into a single, cohesive workflow. Kleboscope offers two complementary report views: Gene‑centric – each gene is shown with all genomes that contain it, together with its frequency, enabling rapid cross‑genome pattern discovery; and Sample‑centric – each isolate gets its own interactive box with typing badges (MLST, K‑locus, O‑locus, hypervirulence), per‑database tables (AMR, Virulence, BACMET, Plasmids), and full mutation details – perfect for clinical reports and patient‑level investigations.

Git repo for Bio::DB::HTS module on CPAN, providing Perl links into HTSlib

RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.

SeqBench is a browser-based workbench of 82 tools for molecular cloning, primer design and sequence analysis: nearest-neighbour melting temperature, oligo dimer and hairpin screening, in-silico PCR, site-directed mutagenesis, restriction mapping, Gibson, Golden Gate and restriction-ligation assembly simulation, plasmid annotation and backbone identification, CRISPR gRNA, HDR donor and base editing design, codon optimisation and CAI, pairwise and multiple alignment, RNA secondary structure, protein properties, Sanger ab1 traces, HGVS conversion and variant annotation. It verifies constructs as well as designing them: re-deriving an assembly from its stated parts and diffing it against the claimed product, aligning sequencing reads back onto a claimed reference, and scoring Golden Gate overhang sets against published ligation-fidelity data. Batch FASTA processing, multi-tool workflows, a conversational tool-calling interface (SeqBench-GPT), a REST API and an MCP server are included.

Browser-based tool to open almost any file that carries sequence — FASTA, FASTQ, GenBank, EMBL, Swiss-Prot, AB1/ABIF, SCF, Clustal, Stockholm, PHYLIP, NEXUS, MSF, PIR, MEGA, GFF3, SAM, BAM, GFA, PDB and ACE — see every sequence inside, pick the ones you want, and save them as FASTA. The format is detected from the file content, not from the extension, so unlabelled or misnamed files still open, and gzip-compressed files are unpacked in place. Records can be filtered by length, name, GC or sequence type, reverse-complemented, transcribed DNA↔RNA or translated to protein, deduplicated and reordered before saving. Runs entirely in the browser — files are never uploaded.

Browser-based viewer for GenBank and GenPept records — .gb, .gbk, .gbff, .gp and plain GenBank text. Renders an interactive linear and circular feature map, including circular plasmid maps, alongside the annotated source text and the nucleotide/protein sequence. Translates CDS features using the record's own genetic code and translation qualifiers, flags where the stored /translation disagrees with a plain translation, and adds optional computed layers: ORF prediction and restriction-site mapping. Drag a range in the sequence band to select it, then copy that stretch — either strand, as DNA or as protein, plain or FASTA. Filters features by type, handles multi-record files, and keeps open records as local sessions, so a closed tab can be picked up where it was left. Runs entirely in the browser — files are never uploaded.