Browse Tools

SBOLDesigner is a Java GUI application for creating, editing, and visualizing synthetic biology genetic designs using the SBOL2 (Synthetic Biology Open Language 2) standard. Supports visual glyph-base

Clair3 -- deep learning-based germline variant caller for long-read sequencing (Oxford Nanopore, PacBio HiFi/CLR, Illumina). Calls SNPs and indels using a two-stage pileup + full-alignment neural netw

Clustal Omega — high-performance multiple sequence alignment tool for protein and DNA sequences using HMM-accelerated pairwise alignment, progressive alignment, and iterative refinement. Supports FAST

CNVpytor — Python tool for copy number variation (CNV) detection from whole-genome sequencing (WGS) BAM/CRAM files. Analyzes read depth signals with adjustable bin sizes, calls deletions and duplicati

fetchChromSizes — UCSC Kent utility for retrieving chromosome size tables (chrom.sizes) for any UCSC genome assembly (hg38, hg19, mm10, mm39, dm6, danRer11, sacCer3, etc.). Queries UCSC MySQL or DAS s

FlashLFQ — ultrafast label-free quantification for mass spectrometry proteomics. Quantifies peptide and protein abundances from MS/MS identifications using peak detection on raw/mzML spectra. Supports

Flye — de novo assembler for single-molecule sequencing reads (PacBio CLR, PacBio HiFi, Oxford Nanopore) using repeat graphs built on approximate sequence matching. Produces polished contigs, GFA repe

GiardiaDB — VEuPathDB genomic resource for the intestinal parasite Giardia lamblia (G. intestinalis, G. duodenalis). Provides gene search, BLAST, genome browsing, functional annotation, ortholog queri

Snippy — rapid haploid variant calling pipeline for bacterial genomics. Maps paired-end or single-end reads to a reference genome using BWA-MEM and Minimap2, calls SNPs, MNPs, and indels via Freebayes

SNP-sites — fast extraction of single nucleotide polymorphism (SNP) sites from multi-FASTA whole-genome alignments. Produces VCF, multi-FASTA (SNP-only), and Phylip output for downstream phylogenetic

Use when working with actc — a Pacific Biosciences (PacBio) command-line tool that aligns CLR subreads to their corresponding CCS (Circular Consensus Sequencing) reads from the same ZMW (zero-mode wav

Use when performing HLA typing from RNA-seq data with arcasHLA. Covers extracting HLA reads from STAR-aligned BAMs, high-resolution genotyping at 6-digit allele level, partial genotyping for low-cover

bedGraphToBigWig converts bedGraph coverage files to bigWig binary format for genome browsers (UCSC, IGV, WashU Epigenome Browser). Essential for ChIP-seq, ATAC-seq, RNA-seq, and WGBS coverage tracks.

Bio-Formats — Java library for reading and writing microscopy image formats. Supports 160+ file formats including OME-TIFF, CZI (Zeiss), LIF (Leica), ND2 (Nikon), VSI (Olympus), and proprietary vendor

Use when working with bioawk — bioawk — AWK with built-in parsers for

blue-crab converts Oxford Nanopore Technology (ONT) sequencing data between POD5 and SLOW5/BLOW5 file formats. Use for long-read genomics workflows that require SLOW5/BLOW5 input (e.g., Buttery-eel ba

Bracken (Bayesian Reestimation of Abundance with KrakEN) — statistical method for computing species-level abundance estimates from Kraken/Kraken2/KrakenUniq taxonomic classifications. Redistributes re

CellPhoneDB — repository of curated receptors, ligands, and their interactions for cell-cell communication analysis from single-cell RNA-seq data. Performs permutation-based statistical analysis (stat

CheckV — assess quality and completeness of metagenome-assembled viral genomes (vMAGs) and contigs. Estimates genome completeness for circular and linear viral sequences using DTR/ITR detection, avera

Corset — C++ tool for clustering de novo assembled transcripts into gene-level groups and producing gene-level counts for differential expression analysis. Groups contigs from Trinity, Trans-ABySS, or

CWLtool — reference implementation of the Common Workflow Language (CWL) for portable, reproducible bioinformatics workflows. Executes CommandLineTool, Workflow, and ExpressionTool descriptors written

cyvcf2 — fast Cython-wrapped htslib library for reading, writing, and querying VCF/BCF variant files in Python. Provides numpy-backed genotype arrays (gt_types, gt_ref_depths, gt_alt_depths, gt_quals,

distiller-nf — Nextflow pipeline for reproducible Hi-C data processing. Aligns Hi-C FASTQ reads with BWA, parses alignments into pairs with pairtools, filters PCR duplicates, and aggregates contacts i

Use when working with eman2 — EMAN2 — comprehensive cryo-EM image processing

Use when preprocessing fMRI data with fMRIPrep. Covers BIDS-compliant preprocessing pipelines, fieldmap correction, ICA-AROMA denoising, confound extraction, surface and volume output spaces, FreeSurf

Use when working with GuacaMol — the benchmarking suite for de novo molecular generation — to evaluate generative models for drug-like molecules. Assesses distribution-learning (17 benchmarks: validit

GuideScan2 — genome-wide CRISPR guide RNA (gRNA) design, specificity analysis, and library construction for Cas9 and Cas12a (Cpf1) in custom genomes. Provides memory-efficient gRNA database building f

HTSlib — C library and command-line utilities for reading, writing, indexing, and manipulating high-throughput sequencing data in SAM, BAM, CRAM, VCF, BCF, and tabix-indexed formats. Provides bgzip bl

HyPhy (Hypothesis Testing using Phylogenies) — open-source software for molecular evolution analysis and natural selection detection. Provides site-level methods (FEL, SLAC, FUBAR, MEME), branch-level

Kaiju is a fast taxonomic classifier for metagenomic sequencing reads using protein-level sequence matching. Translates DNA reads into amino acid sequences and compares against NCBI protein reference

KMC — high-performance disk-based k-mer counting and set operations for genomic sequences. Counts k-mers in FASTQ, FASTA, BAM, and KMC database files with minimal memory usage via disk-based partition

'Use when working with lefse — LEfSe (Linear discriminant analysis Effect

MaxBin2 — metagenomic binning tool that recovers metagenome-assembled genomes (MAGs) from assembled contigs using an expectation-maximization algorithm with marker gene probabilities and coverage info

Meeko — Python interface for AutoDock molecular docking preparation. Parameterizes small-molecule ligands and macromolecular receptors into PDBQT format for AutoDock-GPU and AutoDock-Vina. Handles fle

MOABS (Model Based Analysis of Bisulfite Sequencing) — epigenomics toolkit for DNA methylation calling and differential methylation analysis from WGBS and RRBS experiments. Core tools: mcall (CpG meth

mosdepth — fast BAM/CRAM depth calculation for WGS, exome, and targeted sequencing. Computes per-base depth, mean per-window depth for CNV calling, per-region coverage from BED intervals, coverage dis

NGMLR — long-read mapper for sensitive alignment of PacBio and Oxford Nanopore reads to reference genomes using convex gap-cost scoring. Designed for structural variation detection with SV-aware k-mer

NgsRelate — pairwise relatedness estimation from NGS data using genotype likelihoods. Estimates kinship coefficients, R0/R1/KING-robust statistics, and inbreeding coefficients from VCF/BCF files or AN

Open Babel — open-source cheminformatics toolkit for chemical file format conversion, 3D coordinate generation, molecular fingerprint calculation, substructure and SMARTS pattern searching, descriptor

OrthoFinder — fast, accurate ortholog inference for comparative genomics. Identifies orthogroups, orthologs, gene trees, rooted species trees, and gene duplication events from protein or nucleotide se

Use when working with OWLTools — a Java command-line toolkit for manipulating OWL and OBO biomedical ontologies. Supports graph traversal, subset extraction, reasoner-based inference (Elk, HermiT), SP

PAML — Phylogenetic Analysis by Maximum Likelihood. Suite of programs for phylogenetic analysis of DNA and protein sequences using maximum likelihood. Includes codeml (codon/amino acid models, dN/dS s

Peddy — pedigree and sample QC tool for VCF files. Verifies sample sex from X-chromosome heterozygosity, checks relatedness against PED file expectations, predicts ancestry via PCA against 1000 Genome

Percolator — semi-supervised machine learning tool for rescoring peptide-spectrum matches (PSMs) from shotgun proteomics database searches. Uses target-decoy competition with SVM classification to sep

Use when working with Peregrine (peregrine-2021) — a fast, SHIMMER-based

PhyloBayes — Bayesian MCMC phylogenetic inference software using infinite mixture models (CAT, CAT-GTR) of amino acid or nucleotide substitution. Runs parallel MCMC chains, assesses convergence with b

PhyML — maximum likelihood phylogenetic inference from nucleotide and amino acid sequence alignments. Supports GTR, HKY, K80, JC, and 15+ DNA/protein substitution models, gamma rate heterogeneity (+G)

pigz (Parallel Implementation of GZip) — multi-threaded drop-in replacement for gzip that compresses and decompresses files using multiple CPU cores. Supports gzip, zlib, and single-entry zip formats.

RAxML-NG — maximum likelihood phylogenetic tree inference using iterative SPR moves with libpll likelihood computation. Supports DNA, protein, binary, and multi-state data with partitioned analyses, n

Use when working with resfinder — resFinder — command-line tool for identifying