Free line marker software for linux

Single Marker Association is a simple tool that calculates the single marker association between individual SNP markers and a case/control dichotomy.
Usage:
The tool reads two files as input, the first is a set of case and the second a case of control haplotypes. The format of the files is one line per haplotype, where the SNP data is represented as 0 or 1, separated by white-space.
- The tool outputs a list of statistics for each marker
- The marker number (from left to right in the input data)
- The frequency of the 0 allele for the cases file
- The chi-square contingency table statistics for the marker
- The CDF of the chi-square statistics
- The p-value of the statistics (1-CDF)
Installation:
The SMA tool is written in C++. It should compile on any Unix like system. To install, download the source code and unpack it (tar xzf sma-v.tar.gz, where v is the version number of sma), then run make in the subdirectory sma-v created during unpacking.
Enhancements:
- Support for (unphased) genotype data.

slsnif is a serial line sniffer. It listens to the specified serial port and logs all data coming through it. slsnif works transparently for both the device connected to the serial port and the controlling software for this device. It operates by opening a pseudo tty (pty) and linking it to the actual serial port.
slsnif operates by opening a pty and linking it to the serial port. These are following parameters / options:
1. Serial port to open (required).
2. Name of the file to direct output to (optional, defaults to stdout).
3. Desired baudrate (optional, defaults to 9600 baud).
4. Timestamp On/Off (optional, defaults to Off).
5. Print ascii values in hex On/Off (optional, defaults to Off)
6. Print number of bytes transmitted On/Off (optional, defaults to Off).
7. Optional colors for timestamp, number of bytes transmitted and normal output.
8. Lock port On/Off (optional, defaults to On).
9. Use Unix98 ptys instead of BSD ptys (optional, defaults to BSD style).
10. Second serial port to open. If specified, this port will be used instead of a pty, thus providing an ability to log data between two serial ports.
Enhancements:
- Added ability to resynchronize ports at any time by sending a SIGUSR1 signal to slsnif. Useful for debugging applications that change port parameters mid-way, after starting the transmission. One example is pppd daemon, which sets initial parameters in the chat script, and changes them later, after chat script terminates.
- Added ability to use SYSV (Unix98) ptys instead of BSD ones (see -u and --unix98 parameters). This option can also be turned on/off from rc-file.

Elfelli is a tool to simulate and visualize electric flux lines around arbitrary positioned, electrically charged bodies.
The project is able to export PNG files of the current canvas. Elfelli is written in C++ and uses gtkmm.
Compiling:
To compile Elfelli, you need SCons. In many distributions you will also need the development package of gtkmm (in Debian this is libgtkmm-2.4-dev).
Compiling itself is very simple:
$ scons
Installation:
To install Elfelli, simply type:
$ scons install
By default, it is installed in /usr/local. If you want to change that prefix, alter the install command to:
$ scons install prefix=/install/prefix
Enhancements:
- Its now possible to save and load the current scene as well as changing a bodys charge.

clive is a command line program that extracts videos from YouTube and Google Video websites. The project supports embedded video extraction, and can be used with ffmpeg to re-encode the extracted videos to different video formats (avi, mpeg, flv).

Command Line calculator "CLC" is the calculator that can calculate direct at the Linux console.

Extract the CLCC file to /usr/bin you might need to login as root or equvalent account, to be able to access it whenever you need it.

Then just write CLCC 67+89 and the answer will be presented to you directly.

CLCC calculates from left to right with no exceptions. CLC also have some extra parameters that is sent to CLC using backslash parameters.

CLCC r2 10/3 this will round the result to 2 decimals you can use 1 to 9 if you want to round the sum of.

the r parameter can also be combined with the other parameters but it must be added first like this

CLCC r3c 10/3 - to get 10 diveded with 3 rounded down to 3 decimals.

CLCC is tested with Ubuntu 6.10 and Puppy OS 2.13 but should work with any Linux version in console mode.

The program is developed using Hotbasic for Linux and is Freeware, hope you find it useful, send and email if you have any questions.

Hotbasic is a basic language that compiles into assembler direct, no interpeter that slows down the code, just pure assembler.

So if you want assembler in Linux but doesnt want to code in nasm, HotBasic is the compiler for you.

Metawriter provides an editor for interlinked texts.

It is useful for writing highly structured documentation, or creating a mindmap with link tracking.

Each text is given a name, a title, a group, and a state marker.

The content syntax is similar to that used by a Wiki.

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.