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.
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.
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.
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.
Genetic variants discovery tool
Bioinformatics pipeline for discovery of genetic variants from NGS reads.
docbook2X converts DocBook documents to man and Texinfo format.
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
Tools for accessing and converting various ebook file formats
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".
A modular DNS server. It can be used as a dynamic DNS server, or it can be modified to fetch names from a pre-existing database.
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.
Small, powerful, full featured WYSIWYG editor
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.
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
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
FireEgl's PuTTY -- FuTTY!
FuTTY is a fork of PuTTY and PuTTYTray.
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.
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.
Tools for genomic analysis
BamBam includes numerous tools for analyzing DNA next-generation sequencing data. Tools are provided for calling SNPs and indels, identifying large scale deletions, tabulating counts of mapped reads, methylation analysis, and more. Depends on SAMtools (http://samtools.sourceforge.net/) and BAMtools (https://github.com/pezmaster31/bamtools). Also uses BioPerl, which is included in the download tarball.
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.
Raddle is a network emulation framework. It is particularly useful when testing network management systems or teaching people to use them. Raddle supports ping, SNMP, traceroute, and other protocols.
Computational Suite for Bioinformaticians and Biologists
CSBB is a command line based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux, UNIX and Windows platforms. Currently CSBB provides 16 modules focused on analytical tasks like normalization, visualization, statistics, RNA-SEQ etc.
Computational Suite For Bioinformaticians and Biologists
CSBB is a command line based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux, UNIX and Windows platforms. Currently CSBB provides 17 modules focused on analytical tasks like normalization, visualization, statistics, RNA-SEQ etc.
This project is for maintaining a linux system that concentrates on math, logic, and geometry related softwares.