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.
docbook2X converts DocBook documents to man and Texinfo format.
Genetic variants discovery tool
Bioinformatics pipeline for discovery of genetic variants from NGS reads.
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
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.
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.
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.
Tool to automatically fire regular security scans with Nessus. Compare results of the current scan with the previous scan and report on the delta in a web interface. Main objective of the tool is to make repeated scans more efficient. Not affiliated
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.
DSRE is a project designed to commoditize Internet radio broadcasting. Using DSRE, anyone with webhosting can access the world of online broadcasting, making the hosting of a radio stream no more difficult or expensive than the hosting of an HTML page.
Do you still have PFS:First Choice database files? First Choice was a great DOS-base flat file database program. The program, first2html, reads the file and converts it to HTML, as a TABLE. You can put your First Choice database into a web page!
Abstract Script Engines, or ASE, is a cross-platform and language-independent scripting environment. ASE has an in-process communication mechanism which allows objects to communicate together across language boundaries.
Actor provides a web-enabled, self-service user interface to run your scripts. You run a desktop application to setup your scripts in Actor. Your users get a web site where they access your scripts in a controlled, fail-safe manner.
Apache::ContentHandler is a generic framework for creating mod_perl based applications. It provides a basic event mechanism and a subclassable framework for customizing actions.
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.
BGPWatch is a Linux and BSD background process monitor written in Perl. It is useful for controlling how many processes each user has running , what processes they are running, and what they are allowed to run.
A Web-site concentrating information, reviews, advocacy material and a comparison of Version Control systems, or Source Configuration Management (SCM) systems.
Capitol Realm Controller will provide basic authentication and directory services for Kerberos realms, similar to Microsoft's ActiveDirectory or Novell's NDS. Initially, the main goal will be towards basic POSIX compliance, but advanced features may fo
A collection of utilities, developer tools and libraries developed by the Maize Functional Genomics of Chromatin Consortium