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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

NTHU-CS Maple BBS 2.36 BBS-like editor Besides normal functions, it has some great features for programmers -- goto line (ESC-G) cut & paste cross files (Ctrl-G to see ve.hlp) block shift left/right (ESC-J/K, Ctrl-G to see ve.hlp) parenthesis matching (ESC-[) seaching (Ctrl-S, ESC-n, ESC-p) (matching start of line, case sensitive/in-sensitive, forward/backward) undo line (ESC - '-', or ESC-_ ) undelete lines (ESC-u) ... emacs-like hot-key ve is a tiny editor, about 60K. It's woju's favorite UNIX editor. The most obvious weakness of ve is changing TABs into Spaces. So please don't use ve to edit TAB-important files, such as Makefile, sendmail.cf, syslog.conf... etc.

This port allows to access CP/M file systems similar to the well-known mtools package, which accesses MSDOS file systems. It contains the followin set of tools: * cpmls - list sorted directory with output similar to ls, DIR, P2DOS DIR and CP/M3 DIR[FULL] * cpmcp - copy files from and to CP/M file systems * cpmrm - erase files from CP/M file systems * cpmchmod - change file permissions * cpmchattr - change file attributes * mkfs.cpm - make a CP/M file system * fsck.cpm - check and repair a CP/M file system (only simple errors can be repaired so far). Some images of broken file systems are provided. * fsed.cpm - view CP/M file system * manual pages for everything including the CP/M file system format All CP/M file system features are supported. Password protection is ignored, but a pseudo file [passwd] contains them decrypted.

GXemul is a free instruction-level machine emulator, emulating not only the CPU, but also other hardware components, making it possible to use the emulator to run unmodified operating systems such as NetBSD, OpenBSD, or Linux. A few different machine types are emulated. The following machine types are emulated well enough to run at least one "guest OS": * ARM: CATS (NetBSD/cats, OpenBSD/cats), IQ80321 (NetBSD/evbarm), NetWinder (NetBSD/netwinder) * MIPS: DECstation 5000/200 (NetBSD/pmax, OpenBSD/pmax, Ultrix, Linux/DECstation, Sprite), Acer Pica-61 (NetBSD/arc), NEC MobilePro 770, 780, 800, 880 (NetBSD/hpcmips), Cobalt (NetBSD/cobalt), Malta (NetBSD/evbmips, Linux/Malta) Algorithmics P5064 (NetBSD/algor), SGI O2 (aka IP32) (NetBSD/sgi) * PowerPC: IBM 6050/6070 (PReP, PowerPC Reference Platform) (NetBSD/prep), MacPPC (generic "G4" Macintosh) (NetBSD/macppc) * SuperH: Sega Dreamcast (NetBSD/dreamcast, Linux/dreamcast), Landisk (OpenBSD/landisk)

Asteroid (just one!) is a modern version of the arcade classic Asteroids, using OpenGL, GLUT, and optionally GTK and SDL_mixer. It features a variety of powerups, taunting aliens, 3D textured asteroids, face-melting sound effects, and infinite playability. Controls -------- Use the left and right arrows to turn the ship, x to accelerate, and z to shoot. Pressing p will pause the game, f toggles fullscreen mode, and m mutes and unmutes the audio. There's also a right-click menu if you forget anything. Gameplay -------- I'm not going to explain how to play Asteroids. I will mention that the wireframe octahedra that sometimes drift across the screen are powerups. To collect the powerups, run over them; or you can shoot them for bonus points (if you don't want the benefit of the powerup). You'll have to play the game to figure out the different powerup types.

Evilfinder shows you whether things are evil. By default, the port will install a wrapper called "evilfinder," but you can define WITH_WRAPPER to build the web-oriented default binary only. **** THE PROOF THAT The FreeBSD Project IS EVIL **** T H E F R E E B S D P R O J E C T 20 8 5 6 18 5 5 2 19 4 16 18 15 10 5 3 20 - as numbers 2 8 5 6 9 5 5 2 1 4 7 9 6 1 5 3 2 - digits added \___________/ \________/ \__________/ \_________/ \_/ 3 3 3 6 2 - digits added Thus, "The FreeBSD Project" is 33362. Add 1947, the year Aleister Crowley paid a longer visit to Hell. The result is 35309. Turn the number backwards, and add 1945 - the year Mussolini was executed for the first time. The number is now 92298. Add 9981 to it - this is the year "Scrabble" was invented to promote violence and anger, written backwards - you will get 102279. Subtract 23, the symbol of death. The result will be 102256. Divide the number by 83 - this is the symbol of slavery, backwards. It gives 1232. This number, read as octal, gives 666 - the number of the Beast. This is truly evil. QED. -Adam Weinberger <adamw@FreeBSD.org>

Scm conforms to Revised^5 Report on the Algorithmic Language Scheme and the IEEE P1178 specification. SLIB is a portable Scheme library which SCM uses. SLIB-PSD is a portable debugger for Scheme (requires emacs editor). The init file is hard-coded as /usr/local/lib/scm/Init.scm. Alternatively, one can set the environment variable SCM_INIT_PATH to the pathname of Init.scm. The library files are in /usr/local/lib/scm/slib. Alternatively, one can set the environment variable SCHEME_LIBRARY_PATH to the slib directory. Remember to use a trailing / on the pathname. By default -DSICP is turned on, with the expectation that this is the major reason for this port. This means test.scm will fail on three tests in section 6.1. Where strict R4S compliance is important, recompile without the SICP flag.

[ excerpt from developer's web site ] MIRACL is a Big Number Library which implements all of the primitives necessary to design Big Number Cryptography into your real-world application. It is primarily a tool for cryptographic system implementors. RSA public key cryptography, Diffie-Hellman Key exchange, DSA digital signature, they are all just a few procedure calls away. Support is also included for even more esoteric Elliptic Curves and Lucas function based schemes. The latest version offers full support for Elliptic Curve Cryptography over GF(p) and GF(2m). Less well-known techniques can also be implemented as MIRACL allows you to work directly and efficiently with the big numbers that are the building blocks of number-theoretic cryptography. Although implemented as a C library, a well-thought out C++ wrapper is provided, which greatly simplifies program development. Most example programs (25+ of them) are provided in both C and C++ versions.

p5-MatrixReal is port of the perl module Math::MatrixReal, implementing a matrix of Reals. Math::MatrixReal needs support for operator overloading to support operations on matrixes as though they were just another basic perl type. In addition to the basics (+, -, *) also supported are: matrix norm, matrix transposition, matrix inverse, determinant of a matrix, order and numerical condition of a matrix, scalar product of vectors, vector product of vectors, vector length, projection of row and column vectors, a comfortable way for reading in a matrix from a file, the keyboard or your code, solving linear equations, etc. It also has an implementation of Kleene's algorithm for finding minimal costs for paths in a graph.

Nmap is a utility for network exploration and security auditing. It supports various types of host discovery (determine which hosts are up), many port scanning techniques for different protocols, version detection (determine service protocols and application versions listening behind ports), and TCP/IP stack fingerprinting (remote host OS or device identification). Nmap also offers flexible target and port specification, decoy/stealth scanning, sunRPC scanning, and much more. Also included is Ncat, the nc(1) work-a-like of the Nmap project. Refer to the separate port security/zenmap for those parts of the Nmap toolset which depend on python. The translated manual pages for Nmap are contained in security/nmap-i18n-man. See the web page and the Phrack Magazine article (Volume 7, Issue 51 September 01, 1997, article 11 of 17) http://nmap.org/p51-11.html