SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAMtools provide efficient utilities on manipulating alignments in the SAM format. The main samtools source code repository moved to GitHub in March 2012. For ongoing development since then, see http://github.com/samtools/samtools
Swiss army knife of image processing
GraphicsMagick provides a set of commandline tools and programming APIs for manipulating, editing, and converting raster and vector images. It is derived from ImageMagick, with the objective of providing better stability and performance than ImageMagick while retaining the original MIT/X11 license.
A whole bunch of utilities for primitive manipulation of graphic images. Wide array of converters from one graphics format to another. E.g. from g3 fax format to jpeg. Many basic graphics editing tools such as magnifying and cropping.
Logwatch is a customizable log analysis system. Logwatch parses through your system's logs and creates a report analyzing areas that you specify. Logwatch is easy to use and will work right out of the package on most systems.
UrJTAG aims to create an enhanced, modern tool for communicating over JTAG with flash chips, CPUs, and many more. It is a descendant of the popular openwince JTAG tools with a lot of additional features and enhancements.
The intent behind TorrentSpy is to give the BitTorrent power-user all the information they can get in one place. The primary motivating feature is the ability to see in real time the current number of complete/incomplete users on a torrent.
Tools for accessing and converting various ebook file formats
docbook2X converts DocBook documents to man and Texinfo format.
Genetic variants discovery tool
Bioinformatics pipeline for discovery of genetic variants from NGS reads.
Log analyser for Squid access.log
Screen squid is web-based interface for viewing reports based on Squid proxy server log files. It can be accessed from web-browser through more than 50 reports. No extra files, only DB. All reports generated "on-the-fly".
WideStudio is an Integrated Development Environment (IDE) for building window applications in C++, Ruby, Python an Perl for Windows, MacOSX, Linux, FreeBSD, SOLARIS and other unix and BTRON and T-Engine. This is open and free (under MIT/X Consortiun Lice
Lipi Toolkit is a generic toolkit for online Handwriting Recognition (HWR), and contains tools and algorithms for HWR. The current versions focus on isolated shapes and characters. Details at http://lipitk.sourceforge.net.
The Entropy Gathering Daemon is a portable perl script which provides a source of randomness on systems that lack an in-kernel /dev/random. GnuPG, OpenSSH, and the OpenSSL toolkit can use EGD to seed their random number generators.
Blosxom is a lightweight yet feature-packed weblog application designed from the ground up with simplicity, usability, and interoperability in mind.
LinEd is a line-based text editor written in Perl. It is not designed to write files, but to correct minor errors. When a normal text editor would load an entire file, LinEd will only show a few lines, making finding and rectifying the error a simple job
Small, powerful, full featured WYSIWYG editor
Pretty Damn Quick (PDQ) analytically solves queueing network models of computer and manufacturing systems, data networks, etc., written in conventional programming languages. Generic or customized reports of predicted performance measures are output.
Overview of pre-defined compiler macros for standards, compilers, operating systems, and hardware architectures.
GGI stands for "General Graphics Interface", and it is a project that aims to develop a reliable, stable and fast graphics system that works everywhere. We want to allow any program using GGI to run on any platform requiring at most a recompile.
Collection of several utilities to work with android backups
Project name: android-backup-toolkit URL: https://sourceforge.net/p/android-backup-toolkit/ License: various (see individual projects) Authors: various (see individual projects) This project is simply a compilation of the six following projects, both latest source code and binaries: * android-backup-extractor: https://sourceforge.net/projects/adbextractor/ * android-backup-splitter: https://sourceforge.net/p/adb-split/ * android-timestamp-keeper: https://sourceforge.net/projects/androidtimestampkeeper/ * helium-backup-extractor: https://sourceforge.net/p/heliumbackupextractor/ * no-adb-backup-app-lister: https://sourceforge.net/projects/no-adb-backup-app-lister/ * tar-binary-splitter: https://sourceforge.net/projects/tar-binary-splitter/ All the android utilities are bundled in a single package.
BART Scheduler is a PalmOS application that determines the appropriate BART trains to take between two stations, given an approximate time to leave or arrive.
FireEgl's PuTTY -- FuTTY!
FuTTY is a fork of PuTTY and PuTTYTray.
Run Windows applications on any computer.
WineBOX is an Open Source implementation of the Windows API and a program loader, allowing many unmodified Windows binaries to run on x86-based computers with out need a operative system.
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
Now in Github: https://github.com/dnaase/Bis-tools/tree/master/Bis-SNP BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously. It works for both of single-end and paired-end reads.Specificity and sensitivity has been validate by Illumina IM SNP array. In default threshold 30X data (Phred scale score > 20), it could detect 92.21% heterozygous SNPs with 0.14% false positive rate Cytosine calling is not only based on reference context, so it could detect non-reference cytosine context. Google group for help: http://goo.gl/zL7Nj
MutationFinder is a biomedical natural language processing (NLP) system for extracting mentions of point mutations from free text. MutationFinder achieves high performance (99% precision, 81% recall on blind test data) as an information extraction system