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Bonnie: Filesystem Benchmark Program Bonnie tests the speed of file I/O using standard C library calls. It does reads and writes of blocks, testing for the limit of sustained data rate (usually limited by the drive or controller) and updates on a file (better simulating normal operating conditions and quite dependent on drive and OS optimisations). The per-character read and write tests are generally limited by CPU speed only on current-generation hardware. It takes some 35 SPECint92 to read or write a file at a rate of 1MB/s using getc() and putc(). The seek tests are dependent on the buffer cache size, since the fraction of disk blocks that fits into the buffer cache will be found without any disk operation and will contribute zero seek time readings. I.e. if the buffer cache is 16MB and the Bonnie test file is 32MB in size, then the seek time will come out as half its real value. The seek time includes rotational delay, and will thus always come out higher than specified for a drive.

Dhrystone is a synthetic computing benchmark program developed in 1984 by Reinhold P. Weicker intended to be representative of system (integer) programming. The Dhrystone grew to become representative of general processor (CPU) performance. DMIPS value is result of dhrystone test divided by 1757, results are often reported in DMIPS/MHz. For more information, see http://en.wikipedia.org/wiki/Dhrystone.

dkftpbench is an FTP benchmark program inspired by SPECweb99. The result of the benchmark is a number-of-simultaneous-users rating; after running the benchmark properly, you have a good idea how many simultaneous dialup clients a server can support. The target bandwidth per client is set at 28.8 kilobits/second to model dialup users; this is important for servers on the real Internet, which often serve thousands of clients on only 10 MBits/sec of bandwidth.

This library provides a powerful but simple way to measure sofware performance. It provides both a framework for executing and analysing benchmarks and a set of driver functions that makes it easy to build and run benchmarks, and to analyse their results.

Pybench is an extensible benchmark suite for Python.

Web Polygraph is a benchmarking tool for Web proxies. Polygraph distribution includes a high-performance client and server simulators. The simulators create a stream of HTTP requests that can be routed through a Web proxy. Studying proxy performance under various [stress] conditions is essential for performance tuning, evaluation of new algorithms, analysis of hardware configurations, and comparing available proxy products.

Free, open source molecular viewer and editor for protein structure, DNA structure, PDB, molecular rendering, biological macromolecule. Atoms may be drawn as spheres of different sizes. Bonds may be drawn as cylindrical sticks, conical sticks or as curved surfaces. Five types of slab are available: planar, spherical, semi-spherical, cylindrical and semi-cylindrical. The slab position and thickness are visible in a small window. Atomic bonds as well as atoms are treated as independent drawable objects. and more.

Crux is a software toolkit for molecular phylogenetic inference. It is structured as a set of Python modules, which makes it possible to quickly develop Python scripts that perform unique, non-canned analyses. Features include: * Tree log-likelihoods can be computed under a variety of models, including all specializations of GTR+I+G and mixture models. Tree likelihoods can be computed in parallel via pthreads. * Bayesian Markov chain Monte Carlo (MCMC) methods (with Metropolis coupling) can sample among non-nested models using reversible model jumps. * Crux is capable of simulating character data under any model its likelihood engine is capable of. * The neighbor joining (NJ) and relaxed neighbor joining (RNJ) implementations are among the fastest in existence. * Pairwise distances between sequences can be computed based on percent identity, or using methods that correct for multiple hits (Jukes-Cantor, Kimura, and logDet).

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.

MUSCLE is multiple alignment software for protein and nucleotide sequences. The name stands for multiple sequence comparison by log-expectation. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. Default parameters are those that give the best average accuracy in the published tests. MUSCLE can achieve both better average accuracy and better speed than CLUSTALW or T-Coffee, depending on the chosen options. Citation: Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5): 1792-1797. Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5(1): 113. The NAR paper gives only a brief overview of the algorithm and implementation details. For a full discussion of the method and many of the non-default options that it offers, please see the BMC paper.