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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.

NcFTP is a free set of programs that use the File Transfer Protocol. The main program is simply called "ncftp". There are also separate utility programs for one-shot FTP operations (i.e. for shell scripts and command line junkies); these include "ncftpget", "ncftpput", and "ncftpls". Also included is a batch processing daemon, "ncftpbatch", which is invoked by the "bgget" command from "ncftp" and also the "-b" flag of "ncftpput" and "ncftpget". Lastly, the "ncftpbookmarks" program is a full-screen utility program to manipulate user's FTP bookmarks.

This is not an interface (like "Digest::MD5") but a Perl implementation of MD5. It is written in perl only and because of this it is slow but it works without C-Code. You should use "Digest::MD5" instead of this module if it is available. This module is only usefull for computers where you cannot install "Digest::MD5" (e.g. lack of a C-Compiler).

cclive is a lightweight command line video extraction tool for YouTube and other similar video websites. It is a rewrite of the clive software in C++ with lower system footprint and fewer dependencies. It works closely with the quvi project to workaround the Flash technology that is being utilized by different media hosts to deliver the content. While being primarily a video download tool, it can also be used alongside with some video players, e.g. mplayer, for viewing streamed videos instead of the Adobe flash player.

cparser is a recursive descent C99 parser written in C99. It contains lexer, parser, constructs an AST and does semantic analysis. It is currently used as a frontend to the libFirm intermediate representation, but can be used independently. cparser is able to bootstrap itself. It currently uses an external preprocessor. * fast recursive descent parser, parses C90 and C99 * handles most GCC extensions, e.g. __attribute__, inline assembler, computed goto, statement expressions * handles some MSVC extensions (like declspec) * provides many useful warnings * format string checker for char and wchar_t * unreachable code analysis * missing return statement check, which pinpoints exact location(s) * write-only/-self variables detection * missing and redundant forward declarations * most warnings switches, which are available for GCC * provides concise messages in case of error, for example when encountering misspelled typenames * compiler driver compatible with GCC (-fxxx, -Wxxx, -M, ...) * uses libFIRM for optimization and code generation (devel/libfirm)

This module collects common URI validation routines to make input validation, and untainting easier and more readable. All functions return an untainted value if the test passes, and undef if it fails. This means that you should always check for a defined status explicitly. Don't assume the return will be true. The value to test is always the first (and often only) argument. There are a number of other URI validation modules out there as well. This one focuses on being fast, lightweight, and relatively 'real-world'. i.e. it's good if you want to check user input, and don't need to parse out the URI/URL into chunks. Right now the module focuses on HTTP URIs, since they're arguably the most common.

CMUNGE is a simple tool for encrypting and compacting C source code, while leaving it syntactically and semantically unchanged. It does this by: * Recursively in-lining `user-defined' #include files. * Renaming C identifiers, except those in the C Standard Library, with names like l1 (i.e. letter-l one), l2, l3, etc. * Removing comments and blank lines, converting multiple consecutive whitespace characters (including `\n') into single blanks, removing all unnecessary whitespace between tokens. * Outputting the transformed code in lines of least N characters long, where N is a user-specified minimum line length. It accepts ANSI and K & R C as its input language.

MED stands for "Mod�lisation et �changes de Donn�es", i.e. Data Modelization and Exchanges. MED ��fichier��, c'est�: * Un mod�le d'�change de donn�es commun centr� sur les notions de maillage et de r�sultat. Ce mod�le d�crit quelles sont les donn�es export�es et �chang�es entre les codes. * Une API (Application Programming Interface) d'acc�s aux donn�es qui se pr�sente sous la forme d'une biblioth�que informatique �crite en C et FORTRAN 77. Cette biblioth�que est distribu�e sous licence GNU LGPL. * Des donn�es �chang�es et stock�es dans des fichiers au format HDF (Hierarchical Data Format).

S.C.O.U.R.G.E. is a rogue-like game in the fine tradition of NetHack and Moria It sports a graphical front-end, similar to glHack or the Falcon's eye. I tried to design the 3D UI as a best of both worlds from old to new: It lets you rotate the view, zoom in/out, view special effects, etc. On the other hand I've always liked the old-school isometric games like Exult or Woodward.

LGrind is a descendant of the Unix utility vgrind. It is used to produce a beautified version of your source code using LaTeX. Unlike other packages this is not pure TeX but an external preprocessor. You run e.g. lgrind example.c > example.tex latex example.tex to get a complete listing. Options for producing includable files and pro- cessing embedded listings in LaTeX texts are provided.