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Version 3 of the FASTA packages contains many programs for searching DNA and protein databases and one program (prss3) for evaluating statistical significance from randomly shuffled sequences. Several additional analysis programs, including programs that produce local alignments, are available as part of version 2 of the FASTA package, which is available as the port biology/fasta. FASTA is described in: W. R. Pearson and D. J. Lipman (1988), "Improved Tools for Biological Sequence Analysis", PNAS 85:2444-2448; W. R. Pearson (1996) "Effective protein sequence comparison" Meth. Enzymol. 266:227-258; Pearson et. al. (1997) Genomics 46:24-36; Pearson, (1999) Meth. in Molecular Biology 132:185-219. The FASTA3 suite is distributed freely subject to the condition that it may not be sold or incorporated into a commercial product.

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.

Tinker is a set of small programs for doing general purpose molecular modeling calculations. Tools are included for energy minimizations, geometry calculations, simulated annealing, molecular dynamics, and molecular analysis calculations. Tools for converting coordinate sets are also provided. Tinker employs several force fields and minimization techniques. This port sets the maxatm value to 2500 atoms. This should be sufficient for most molecular systems. Should you need to work with larger systems you can set the maxatm parameter in the sizes.i file located in the tinker/source directory and recompile. Note that if it is set too large that tinker programs will abort and core dump. For more information about Tinker see:

This simple tool reads a source file with TASM syntax and converts it to AT&T syntax. The AT&T syntax is widely used by GNU tools, in particular the GAS(AS) interpreter and GCC compiler. The TASM syntax is used by many commercial compilers and disassemblers, ie. NASM, MASM, Visual Studio or IDA Pro. Ta2As can automate most of the conversion, but it still isn't perfect - some correction have to be made manually before the code compiles. This tool was originally written by Frank van Dijk and released by SPiRiT group; this is continuation of his work, although not much of the original code remains.

postgresql-relay can be used to as a single point of origin for all your databases. Instead of having to remember (or modify in case of changes) all the names of your databases, on which machines and on which ports they are running, you only need to remember one machine and the name of the database. The postgresql-relay will then forward the connection to the proper database on the proper port of the proper server. No more changes in the hundreds of clients and scripts!

TOra is an open-source multi-platform database management GUI that supports accessing most of the common database platforms in use, including Oracle, MySQL, and Postgres, as well as limited support for any target that can be accessed through Qt's ODBC support. In addition to regular query and data browsing functionality, it includes several additional tools useful for database administrators and developers - which aims to help the DBA or developer of database application. Features PL/SQL debugger, SQL worksheet with syntax highlighting, DB browser and a comprehensive set of DBA tools.

KchmViewer is a chm (MS HTML help file format) viewer. Unlike most existing CHM viewers for Unix, it uses Trolltech's Qt widget library, and does not depend on KDE or Gnome. However, it may be compiled with full KDE support, including KDE widgets and KIO/KHTML. The main advantage of KchmViewer is non-english language support. Unlike others, KchmViewer in most cases correctly detects help file encoding, correctly shows tables of context of russian, korean, chinese and japanese help files, and correctly searches in non-english help files.

The Open On-Chip Debugger (OpenOCD) aims to provide debugging, in-system programming and boundary-scan testing for embedded target devices. OpenOCD uses a "hardware interface dongle" to communicate with the JTAG (IEEE 1149.1) compliant taps on your target board. OpenOCD currently supports many types of hardware dongles: USB based, parallel port based, and other standalone boxes that run OpenOCD internally. It allows MIPS, ARM7, ARM9, XScale and Cortex based cores to be debugged via the GDB protocol. Flash writing is supported for external CFI compatible NOR flashes, NAND and several internal flashes.

Fujaba Tool Suite 4 The primary topic of the Fujaba Tool Suite project is to provide an easy to extend UML and Java development platform with the ability to add plug-ins. * Fujaba Tool Suite combines UML class diagrams and UML behaviour diagrams to a powerful, easy to use, yet formal system design and specification language. * Furthermore the Fujaba Tool Suite supports the generation of Java sourcecode out of the whole design which results in an executable prototype, ideally. * Moreover the way back is provided, too (to some extend so far), so that Java sourcecode can be parsed and represented within UML.

This set of scripts allows to work locally on Subversion-managed projects using the Mercurial distributed version control system. Why use Mercurial? You can do local (disconnected) work, pull the latest changes from the SVN server, manage private branches, submit patches to project maintainers, etc. And of course you have fast local operations like "hg log", "hg annotate"... Three scripts are provided: * hgimportsvn initializes an SVN checkout which is also a Mercurial repository. * hgpullsvn pulls the latest changes from the SVN repository, and updates the Mercurial repository accordingly. It can be run multiple times. * hgpushsvn pushes your local Mercurial commits back to the SVN repository.