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Phrap is a program for assembling shotgun DNA sequence data. Among other features, it allows use of the entire read and not just the trimmed high quality part, it uses a combination of user-supplied and internally computed data quality information to improve assembly accuracy in the presence of repeats, it constructs the contig sequence as a mosaic of the highest quality read segments rather than a consensus, it provides extensive assembly information to assist in trouble-shooting assembly problems, and it handles large datasets. This package also contains Swat and Cross_match. Swat is a program for searching one or more DNA or protein query sequences against a sequence database, using (an efficient implementation of) the Smith-Waterman-Gotoh algorithm. Cross_Match is a general-purpose utility based on Swat for comparing any two sets of DNA sequences, and it can be used to: * produce vector-masked versions of a set of reads * compare a set of cDNA sequences to a set of cosmids * compare contigs found by two altanative assembly procedures to each other * compare phrap contigs to the final edited cosmid sequence.

Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files. Trace data is read from chromatogram files in the SCF, ABI, and EST formats, even if they were compressed using gzip, bzip2, or UNIX compress. Quality values are written to FASTA format files or PHD files, which can be used by the Phrap sequence assembly program in order to increase the accuracy of the assembled sequence. Base calling and quality value accuracies tested for: ABI models 373, 377, and 3700 Molecular Dynamics MegaBACE LI-COR 4000 Base calling accuracies tested for: ABI model 3100 Beckman CEQ It contains also a data evaluation program called 'daev'. See DAEV.DOC for more information. You must obtain the tarball via e-mail to build. See the web site below.

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI). Citation: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008)

Trimmomatic performs a variety of useful trimming tasks for illumina NGS paired-end and single ended data.

"Wise2 is package that is focused on comparing DNA sequences at the level of its conceptual translation, regardless of sequencing error and introns. This really is a rewrite of the old wisetools package, which I wrote about 3 years ago. It can compare a single protein or a profile HMM to a genomic DNA sequence, and predict a gene structure. This is algorithm, called genewise, is one of the algorithms available in Wise2. There are other algorithms focused on EST data rather than genomic data, as well as some other algorithm curios." - from the web site (Ewan Birney)

Alliance is a complete set of free CAD tools and portable libraries for VLSI design. It includes a VHDL compiler and simulator, logic synthesis tools, and automatic place and route tools. A complete set of portable CMOS libraries is provided. Alliance is the result of a twelve year effort spent at ASIM department of LIP6 laboratory of the Pierre et Marie Curie University (Paris VI, France).

Dinotrace is a signal waveform tracing tool that supports traces in the form of Verilog Value Change Dump (VCD), ASCII, Verilator, Tempest CCLI, COSMOS, Chango and Decsim Binary. Dinotrace is also equipped with an interface to GNU Emacs. Dinotrace was conceived in the early 1980's by Allen Gallotta at Digital Equipment Corporation, who wrote the code and supported it through version 4.2. When created, it was the first graphical display tool for the simulators being designed at Digital.

Jspice3 is a circuit simulator developed to meet the needs of researchers working with superconducting Josephson junction circuits, yet the program has the flexibility and power to meet the needs of other technologies. Jspice3 is an adaptation of the Berkeley Spice3f4 program, with added features. One added feature is a built-in graphical input front end for schematic capture. While displayed, simulations can be run and data plotted through this graphical interface. While not as powerful or as pretty as the Xic graphical interface, it holds its own in functionality. A significantly enhanced output plotting capability is provided, and Jspice3 has enhanced script interpretation capability.

A IC/MEMS layout editor. Features: all angle, font generator, macros, boolean operations, design rule checker, crossplatform compatible, supported formats:Calma GDSII, OASIS (Open Artwork System Interchange Standard), DXF, CIF (Caltech Intermediate Form)

NETGEN is an automatic 3D tetrahedral mesh generator. It accepts input from constructive solid geometry (CSG) or boundary representation (BRep) from STL file format. The connection to a geometry kernel allows the handling of IGES and STEP files. NETGEN contains modules for mesh optimization and hierarchical mesh refinement.