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Ultra-fast, sensitive search and clustering suite for protein and nucleotide sequence sets.

A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files.

A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools.

A compressor of common genomic file formats (BAM, CRAM, FASTQ, VCF etc).

samtools/bcftools are a suite of tools for manipulating NGS data and can be used to call variants.

Fast and accurate protein structure search using a learned 3Di structural alphabet (VQ-VAE) that discretizes tertiary interactions into structural tokens, enabling protein-universe-scale structural alignment at sequence-search speeds (4-5 orders of magnitude faster than DALI/TM-align) and underpinning many AI4S tools such as SaProt, ESMAtlas search, and AFDB clustering pipelines (Steinegger Lab, Nature Biotechnology 2023)

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.

A Swiss Army knife for genome arithmetic.

Minimap2 is an pairwise aligner for genomic and spliced nucleotide sequences. It can perform the assembly-to-assembly alignment, and works with gzip'd FASTQ, FASTA formats. It also finds overlaps between long-reads.

metilene³ is a computational tool for identifying Differentially Methylated Regions (DMRs) across multiple conditions, supporting both supervised and unsupervised analyses, and enables the construction of Differentially Methylated Trees for epigenetic relationship inference and sample clustering.

De novo assembler for single molecule sequencing reads using repeat graphs.

the wavefront alignment algorithm (WFA) which expoit sequence similarity to speed up alignment

BWA-MEM drop-in replacement: 2-3x faster, 2-5x cheaper, 100% identical output on standard CPUs.

lumpy: a general probabilistic framework for structural variant discovery.

Pairwise SNP distance matrix from a FASTA sequence alignment

SIMD C library for global, semi-global, and local pairwise sequence alignments

Minigraph is a sequence-to-graph mapper and graph constructor. For graph generation, it aligns a query sequence against a sequence graph and incrementally augments an existing graph with long query subsequences diverged from the graph.

Toolkit for processing sequences in FASTA/Q formats.

A database system designed to store, organize, and manage large-scale nucleotide sequencing read data (like PacBio reads) for the Dazzler genome assembler

A fuzzy Bruijn graph approach to long noisy reads assembly

Displaying sequence statistics for next-generation sequencing.

Create an index on a compressed text file.

FASTQ/A short-reads pre-processing tools: Demultiplexing, trimming, clipping, quality filtering, and masking utilities.

**Comes with samtools!** - Reads simulator.

Finds SNP sites from a multi-FASTA alignment file.

A wee tool for random access into BGZF files.

Comprehensive set of programs for phylogenetic analyses; available for PC and Mac; source code available for easy compiling in UNIX.