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glmark2 is a benchmark for OpenGL (ES) 2.0. It uses only the subset of the OpenGL 2.0 API that is compatible with OpenGL ES 2.0.

SysBench is a modular, cross-platform and multi-threaded benchmark tool for evaluating OS parameters that are important for a system running a database under intensive load. The idea of this benchmark suite is to quickly get an impression about system performance without setting up complex database benchmarks or even without installing a database at all. Current features allow to test the following system parameters: * file I/O performance * scheduler performance * memory allocation and transfer speed * POSIX threads implementation performance * database server performance (OLTP benchmark) Primarily written for MySQL server benchmarking, SysBench will be further extended to support multiple database backends, distributed benchmarks and third-party plug-in modules.

BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and cross-species protein alignments. BLAT is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences. (Source: Kent, W.J. 2002. BLAT -- The BLAST-Like Alignment Tool. Genome Research 4: 656-664. http://dx.doi.org/10.1101/gr.229202) BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome (but not the genome itself) in memory. Since the index takes up a bit less than a gigabyte of RAM, BLAT can deliver high performance on a reasonably priced Linux box.

Consed is a tool for viewing and editing sequence assemblies made by phrap, and includes Autofinish which will automatically choose finishing reads.

A standalone program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. The program generates accurate gene structures, even in the presence of substantial polymorphisms and sequence errors, without using probabilistic splice site models. Methodology underlying the program includes a minimal sampling strategy for genomic mapping, oligomer chaining for approximate alignment, sandwich DP for splice site detection, and microexon identification with statistical significance testing.

p5-Bio-Das-Lite is an implementation of a client for the DAS protocol (XML over HTTP primarily for biological-data).

Bioperl-run contain modules that provides a PERL interface to various bioinformatics applications. This allows various applications to be used with common Bioperl objects.

Samtools implements various utilities for post-processing alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer.

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

atlc is a program designed for finding the properties (characteristic impedance, inductance per meter, capacitance per meter, velocity factor, electric field distribution) of any transmission line with 2 or 3 conductors (i.e. a normal line or coupler). It uses the finite difference method to determine these properties, and can handle any cross section. The program atlc needs to know shape of the transmission line's cross section. This cross section is stored in a data file, which happens to be a Windows bitmap file. The bitmap file is read by atlc, following which the program performs the analysis. Look in /usr/local/share/examples/atlc for some examples.