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Siege is an http regression testing and benchmarking utility. It was designed to let web developers measure the performance of their code under duress, to see how it will stand up to load on the internet. It lets the user hit a web server with a configurable number of concurrent simulated users.

The program thrulay is used to measure the capacity, delay, and other performance metrics of a network by sending a bulk TCP or UDP stream over it. Special features of thrulay include: * For TCP, ability to measure round-trip delay along with throughput * For UDP, ability to measure - one-way delay, with quantiles - packet loss - packet duplication - reordering * For UDP, the ability to send precisely positioned true Poisson streams (microsecond errors in sending times) * Human- and machine-readable output (ready to be fed to gnuplot)

The Unix Benchmark Utility "ubench" is an attempt to introduce a single measure of perfomance among computer systems running various flavors of Unix operation system. The current development release tests only CPU(s) and memory. In the future releases there will be tests added for disk and TCP/IP. Ubench is taking advantage of multiple CPUs on an SMP system and the results will reflect that. o Ubench is executing rather senseless mathematical integer and floating-point calculations for 3 mins concurrently using several processes, and the result Ubench CPU benchmark. o Ubench will spawn about 2 concurrent processes for each CPU available on the system. This ensures all available raw CPU horsepower is used. o Ubench is executing rather senseless memory allocation and memory to memory copying operations for another 3 mins concurrently using several processes, and the result Ubench MEM benchmark.

ARIADNE is a package of two programs, ariadne and prospero, that compare protein sequences and profiles using the Smith-Waterman algorithm, and assesses statistical significance using a new accurate formula, described in Mott, 2000, "Accurate Formula for P-values of gapped local sequence and profile alignments" J. Mol Biol. 300:649-659. The sequence/profile comparison algorithms used in ARIADNE are standard, and are probably not the fastest implementations available. The novel part is the method for determining statistical significance, which will give thresholds of significance that are accurate to within 5% 95% of the time. The package is written in ANSI C. You are free to incorporate the method used for assessing statistical significance into third-party code, provided you cite the above reference. The routines for assessing significance are all in gaplib.c

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

Visualizing the results of molecular orbital calculations 1) MO program: gaussian, gamess, mopac, etc. 2) display molecule in 3D: geo-opt, single-point, nomal mode (animation) 3) density: contour plot or 3D view for electron density and MO coefficient Everything what you want about MO calculation can be seen. By the distribution policy of the author; * Only the latest version is supplied. * Users must get the `distfiles' from the original site. * Do not re-distribute the source and the executable. * Using a not-so-latest version is prohibited, because the author may only respond about the latest version.

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.

Gperiodic displays a periodic table of the elements, allowing you to browse through the elements, and view detailed information about each element.

GRAPPA: Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms This suite of programs implements the approach to phylogeny reconstruction from gene orders described in the paper Moret, B.M.E., Wyman, S., Bader, D.A., Warnow, T., and Yan, M., ``A detailed study of breakpoint analysis,'' Proc. 6th Pacific Symp. Biocomputing PSB 2001, Hawaii (2001). In its current state, "grappa" allows one to explore either the space of all possible trees on n labelled leaves or the space of all such trees that obey (are refinements of) a particular constraint tree. "invdist" takes the first two genomes in the input file and returns their inversion distance. "distmat" prints the inversion and breakpoint distance matrices.

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism.