OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.

RNA-seq aligner

A versatile pairwise aligner for genomic and spliced nucleotide sequences

MMseqs2: ultra fast and sensitive search and clustering suite

SRA Tools

bedtools - the swiss army knife for genome arithmetic

Advanced and Fast Data Transformation in R

BWK awk modified for biological data

Official home of genome aligner based upon notion of Cactus graphs

A Python module to customize the process title

Sequence-to-graph mapper and graph generator

Fast and accurate de novo assembler for long reads

Align proteins to genomes with splicing and frameshift

🔬 BEDOPS: high-performance genomic feature operations

GenomeTools genome analysis system.

Long read / genome alignment software

Reads simulator

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Primer3 is a command line tool to select primers for polymerase chain reaction (PCR).

haplotypic duplication identification tool

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

UCSC Genome Browser source. "beta" is released version / "master" is testing.

Tools for manipulating sequence graphs in the GFA and rGFA formats

Fast and accurately polish the genome generated by long reads.

software tools for haplotype assembly from sequence data

Tools test whether admixture occurred and more

Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment

Constructing a pangenome gene graph

WFA-lib: Wavefront alignment algorithm library v2

Tandem Repeats Finder: a program to analyze DNA sequences