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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

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.

BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads.

CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.

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

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

LAMARC (Likelihood Analysis with Metropolis Algorithm using Random Coalescence) is a package of programs for computing population parameters such as population size, population growth rate and migration rates. It does this by using likelihoods for samples of data (sequences, microsatellites, and electrophoretic polymorphisms) from populations.

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.