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The STREAM benchmark is a simple synthetic benchmark program that measures sustainable memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels. Documentation can be found at: http://www.cs.virginia.edu/stream/ref.html

Super Smack is a benchmarking, stress testing, and load generation tool for MySQL (and PostgreSQL). Super Smack was originally written by Sasha Pachev, and then hosted and maintained by Jeremy Zawodny.

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour.

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour.

Chemeq is a basic standalone filter written in C++ language, flex and bison. It takes strings like: 2H2 + O2 ---> 2 H2O and can output pretty LaTeX code, useful messages and much more. It aims to be embeddable in education tools.

gff2ps is a script program developed with the aim of converting gff-formatted records into high quality one-dimensional plots in PostScript. Such plots maybe useful for comparing genomic structures and to visualizing outputs from genome annotation programs.

MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.

HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing data. It is the core library used by samtools and bcftools.

Migrate estimates effective population sizes and past migration rates between two or "n" populations assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. The n-population migrate can use sequence data, microsatellite data or electrophoretic data.