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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.

The NCBI (National Center for Biotechnology Information) development toolkit, containing various libraries needed by NCBI applications, as well as a software suite containing, amongst other things, NCBI BLAST 2.0. From the README: The NCBI Software Development Toolkit was developed for the production and distribution of GenBank, Entrez, BLAST, and related services by NCBI. We make it freely available to the public without restriction to facilitate the use of NCBI by the scientific community. However, please understand that while we feel we have done a high quality job, this is not commercial software. The documentation lags considerably behind the software and we must make any changes required by our data production needs. Nontheless, many people have found it a useful and stable basis for a number of tools and applications.

Bio::SCF module allows you to read and update (in a restricted way) SCF chromatographic sequence files. It is an interface to Roger Staden's io-lib. See the installation directions for further instructions.

"The SEQIO package is a set of C functions which can read and write biological sequence files formatted using various file formats and which can be used to perform database searches on biological databases." - from the README file

ADMS is a code generator that converts electrical compact device models specified in high-level description language into ready-to-compile C code for the API of spice simulators.

Electric is a sophisticated electrical CAD system that can handle many forms of circuit design, including: - Custom IC layout (ASICs) - Schematic drawing - Hardware description language specifications For real functionality, one should consider installing support simulation software such as cad/spice.

GTKWave is a fully featured GTK+ based wave viewer for Unix and Win32 which reads LXT, LXT2, VZT, and GHW files as well as standard Verilog VCD/EVCD files and allows their viewing.

Impact is an explicit Finite Element Program which simulates dynamic impact events. It has a range of elements, contact handling and different material laws. Models can be created and viewed with external programs or the included postprocessor.

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)

LeoCAD is a CAD program that can be used to create virtual LEGO models. It has an easy to use interface and currently features over 4000 different pieces created by the LDraw community.