Free linkage software for linux

Kylie is a web browser. It does text, images, tables and soon forms. It doesnt know css, frames or scripting. And its neither fast nor cute. Thats why it is version 0.0.x.
Parsing
The HTML parser in MwHtmlParser.c creates a linked list of all the
nodes: wordparts, whitespace and special tags.
Newline immediately before end tag is ignored. Newline immediately after
start tag is ignored.
Composite objects (currently limited to TABLE, ROW and CELL, but
frames belong there too) branch the list so it actually becomes a tree.
Displaying
When the widget gets the list back, it lays out the boxes by assigning
width and height and placing them in a line from left to right. If
there is too little space left for another box, start over on a new
line.
In a second pass the objects are drawn which are located in the
currently visible part of the window.
Two callbacks in the widget, begin_a and
end_a, handle and tags. The coordinates are put in the
a_href or a_name tables depending on their HREF or NAME values.
Composite objects are displayed by recursively drawing the list
of children.
Navigation
There are two linked lists for backwards and forwards navigation.
Each time we visit a link, the current url is added to the backwards
lists and the forwards list is cleared, *except* when we visit the
link by clicking the back button. In that case the current url is
added to the forwards list instead.
Type 1 fonts
If Mowitz was compiled with t1lib support, Kylie can take advantage
of it out of the box. The standard fonts.txt file is used for font
management. Antialias is not supported.
IO
The IO is split into different modules with narrow interfaces. The
modules are:
io.c: Register protocol drivers, normalize urls, cache documents.
External linkage: load_url.
http.c: Fetch documents over http. The only symbol with external
linkage is load_http, which should *only* be called from io.c.
file.c: Fetch local file or predefined "documents".
External linkage: load_file and load_about.
FTP is currently not implemented.
None of this belongs in the widget code. The widget should only
have the bare minimum required to render stuff in a window.
The widget will probably eventually move over to Mowitz.
It should suffice to have url resource that is a string to give
to a loader function.
This function can also be set through a resource and defaults to
a function which loads the file from the local file system using
the url as filename.
Everything else belongs in the application.
Images
The file image.c contains a small, stack-oriented library of functions
which can perform a variety of operations on images. The only thing
were using it for at the moment is to load images, usually with
the help of external applications such as the netpbm kit.
An advantage to this approach is that we can display many types of
images. In the future we will also be able to manipulate images in
more ways than we are using now.
The disadvantage is that it is relatively slow. This is mainly due
to the fact that we have to convert between the librarys internal
format, image, and the format X understands, XImage. It should be
possible to help the situation somewhat by caching the XImage; the
current cache implementation only caches the image.
Enhancements:
- Implemented < select > < option >, < optgroup > and < textarea >.
- Speeded up object_between and add_object_box radically.
- Fixed the combo box so it stores history instead of crashing.
- Added a 30 second timeout to the connect() call in http.c.
- Display an error message rather than crashing when a document cant be loaded. Create widgets for (some) form controls.
- Suppress garbage (i.e. extra spaces or words) between < table > and first < tr >.
- Documented table code (in README).

B::LintSubs is a Perl compiler backend to check sub linkage.

SYNOPSIS

perl -MO=LintSubs [FILE] [-e PROGRAM]

When using use strict, subroutine names are not checked at the callsite; this makes the following a perfectly valid program at compiletime, that only blows up at runtime

use strict;
foobar();

When using the B::LintSubs checker instead, this is detected:

$ perl -MO=LintSubs -e use strict;
foobar();
Undefined subroutine foobar called at -e line 2

Imported functions from other modules are of course detected:

$ perl -MO=LintSubs -e use strict;
use List::Util qw( max );
$_ = max( 1, 2, 3 )
-e syntax OK

In order to handle situations where external code is conditionally referenced at runtime, any fully-qualified references to other functions are printed with a warning, but not considered fatal. The programmer is assumed to Know What He Is Doing in this case:

$ perl -MO=LintSubs -e if( 1 ) { require Data::Dumper;
Data::Dumper::Dump( "Hello" ) }

Unable to check call to Data::Dumper::Dump in foreign package at -e line 1

-e syntax OK

Major Features:

1. Better Thunderbird integration
2. emailtask linkage
3. Integration with the Thunderbird address book
4. iMIP support (meeting invitations)
5. Improved CalDAV support
6. Cached calendar support for offline calendar use
7. Device synchronization

Enhancements:

• Events spanning days now have a visual indicator indicating them as connected events
• When reloading a remote calendar a progress indicator is now shown
• The so-called "minimonth" (small calendar month in the upper left) has been given a visual overhaul
• The calendar views (day, week, multiweek, month) have been given a visual overhaul
• The today pane can now be displayed in calendar mode and task mode as well
• CalDAV support and interoperability with various CalDAV servers has been improved
• iMip/iTip support (support for email invitations) has been greatly improved
• The application stability and memory consumption has been greatly improved
• Lightning 0.9 is intended to be the last release for the Thunderbird 2 series. For the future we are planning to integrate Lightning fully into the upcoming Thunderbird 3 release
• A full list of changes that have gone into this release can be found on The Rumbling Edge website

Requirements:

• Software Requirements Please note that Linux distributors may provide packages for your distribution which have different requirements.
• • Linux kernel - 2.2.14 or higher with the following libraries or packages:
  • glibc 2.3.2 or higher
  • XFree86-3.3.6 or higher
  • gtk+2.0 or higher
  • fontconfig (also known as xft)
  • libstdc++5 (Many modern Linux distributions only package libstdc++6, which is incompatible with Lightning. Therefore please install the package "libstdc++5" or "compat-libstdc++" on your system before installing Lightning)
• Minimum Hardware
• • Intel Pentium II or AMD K6-III+ 233 MHz CPU (Recommended: 500MHz or greater)
  • 64 MB RAM (Recommended: 128 MB RAM or greater)
  • 52 MB hard drive space

GeneRecon is a software package for linkage disequilibrium mapping using coalescent theory. GeneRecon project is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps.
GeneRecon explicitly models the genealogy of a sample of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position.
GeneRecon is written in C++ and Guile Scheme and is available as source code (under the GNU General Public License, GPL) and as binary versions as Linux RPM files.
The source code has been successfully compiled on various Linux and UNIX systems, under OS X and under Windows with Cygwin.
As I have only limited access to architectures other than Linux, it is not possible for me to make binary distributions for other platforms, but if anyone is willing to build the distributions I will be more than happy to put them on this site.
Installation:
$ tar zxf generecon-version.tar.gz
$ cd generecon-version
$ ./configure
$ make
$ make check
$ make install
Usage:
GeneRecon is started from the command-line; the input data and parameters for the analysis are described in one or more configuration scripts written in the Scheme programming language. Starting GeneRecon with the configuration script input.scm is done as:
$ generecon input.scm
Run generecon --help to get a complete list of command-line options accepted by GeneRecon, or see Getting Started for a quick guide to running GeneRecon.
Enhancements:
- This version fixes an incorrect prior on the coalescent tree that resulted in very long convergence times.
- The fix greatly improves both accuracy and number of iterations needed for accurate mapping.

Oolaboola is an opensource system for mixing sound files in real-time, while varying their rate of play, amplitude level, etc. In other words, Oolaboola is a digital DJ tool.
Main features:
- Distributed under the terms of the GNU General Public License
- The cross-fader never wears out! :)
- Plays .wav files of various formats.
- Can use MIDI input
- Digital file output.
- Set and goto marks.
- Create loops
- Can record your actions for later playback
- Efficient (mixing two files takes about a Pentium 50 :)
- Low latency (time between your action and the change in output)..down to 1/100th second depending on the limits of your OS/hardware.
- Separate output to `cue channel
- Control rate-of-play..from 0 to 2 X in increments of .001
- Modify its behavior with a python rc file
Enhancements:
- fixes a few bugs, mostly build and linkage problems many people were having.

bigFORTH is a native code Forth. bigFORTH/MINOS is available for Linux and Windows 95/98/NT under GPL. The most striking feature is the graphical user interface MINOS (GUI in Forth) and the form editor Theseus (Theseus is still beta).
Main features:
- Powerful compiler: bigFORTH is a 32 bit system. The compiler generates optimized native code for the i386. You can create turnkey applications for sure. bigFORTH fully complies to ANS Forth.
- Versatile tools: multitasker; source-able decompiler; source level debugger (even using optimized macros) with single step and trace, as many breakpoints as you want; post mortem dump and return stack trace; Pentium-MMX-assembler/disassembler...
- Editor: multi-window editor for screen- and stream-files.
- Extensive libraries: extensive and comfortable file interface (with definitions for the most common Unix commands) ease work even on a big hard disk. System calls and linkage to dynamic libraries are supported. Printer support for listings and session protocols; fast and accurate FP-arithmetics, a "state of the art" memory management, that doesnt capitulate from complex memory structures, graphical user interface (MINOS GUI), object oriented Forth and more...
- Transparency: All sources, including kernel and target compiler in the standard distribution, give the Forth wizard everything they want.
- Modular Forth: bigFORTH is modulary. Separate compilation is possible, small applications are easy to create. Modules have no arbitrary limit in size.
MINOS is a graphic user interface (GUI) for X, written for bigFORTH-Linux and bigFORTH-Win32. It includes a rapid GUI developement editor (Theseus).
MINOS is available under the GPL, not the LGPL. I want to stress that this means you cannot develop applications with it that are not either under the GPL, or distributed seperately as sources, just as with other GPLed libraries (for example, readline).
For people wanting to develop applications with it that are under different licencing conditions, a [html]commercial licence is available at request so that MINOS can be a choice for proprietary systems, too. Ill certainly give major contributors a fair share.

Blossoc is a linkage disequilibrium association mapping tool that attempts to build (perfect) genealogies for each site in the input, score these according to non-random clustering of affected individuals, and judge high-scoring areas as likely candidates for containing disease affecting variation.
Building the local genealogy trees is based on a number of heuristics that are not guaranteed to build true trees, but have the advantage over more sophisticated methods of being extremely fast. Blossoc can therefore handle much larger data sets than more sophisticated tools, but at the cost of sacrificing some accuracy.
Installation:
Blossoc is written in C++ and is available as source code (under the GNU General Public License, GPL) and as binary versions as Linux RPM files. The source code has been successfully compiled on various Linux and UNIX systems. As I have only limited access to architectures other than Linux, it is not possible for me to make binary distributions for other platforms, but if anyone is willing to build the distributions I will be more than happy to put them on this site.
Usage:
Blossoc is started from the command-line and takes, as input, a file containing the positions of markers and a file containing haplotype data.
The format of the haplotype file is: One line per haplotype, where a haplotype is represented as a list of space-separated alleles, and each allele represented as either a 0 or a 1.
The first column is a pseudo-allele used for the case/control dichotomy: a 0 in the first column is taken to mean that the haplotype is a control haplotype and a 1 at the first column is taken to mean that the haplotype is a case haplotype.
Run blossoc --help to get a complete list of command-line options accepted by Blossoc.
Enhancements:
- This version adds support for unphased genotype data through a perfect-phylogeny haplotyping algorithm.
- If enabled, the release will also support the SNPfile binary format.