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Jalview is a multiple alignment editor written in Java. It is used widely in a variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) and is also available as a general purpose alignment editor. o Reads and writes alignments in a variety of formats o Gaps can be inserted/deleted using the mouse. o Group editing (insertion deletion of gaps in groups of sequences). o Removal of gapped columns. o Align sequences using Web Services (Clustal, Muscle...) o Amino acid conservation analysis similar to that of AMAS. o Alignment sorting options (by name, tree order, percent identity, group). o UPGMA and NJ trees calculated and drawn based on percent identity distances. o Sequence clustering using principal component analysis. o Removal of redundant sequences. o Smith Waterman pairwise alignment of selected sequences. o Web based secondary structure prediction programs (JNet). o User predefined or custom colour schemes to colour alignments or groups. o Sequence feature retrieval and display on the alignment. o Print your alignment with colours and annotations. o Output alignments as HTML pages, images (PNG) or postscript (EPS). If you use Jalview in your work, please quote this publication. Clamp, M., et al. (2004), The Jalview Java Alignment Editor. Bioinformatics, 12, 426-7

Apache Pig is a platform for analyzing large data sets that consists of a high-level language for expressing data analysis programs, coupled with infrastructure for evaluating these programs. The salient property of Pig programs is that their structure is amenable to substantial parallelization, which in turns enables them to handle very large data sets. At the present time, Pig's infrastructure layer consists of a compiler that produces sequences of Map-Reduce programs, for which large-scale parallel implementations already exist (e.g., the Hadoop subproject). Pig's language layer currently consists of a textual language called Pig Latin, which has the following key properties: -- Ease of programming. It is trivial to achieve parallel execution of simple, "embarrassingly parallel" data analysis tasks. Complex tasks comprised of multiple interrelated data transformations are explicitly encoded as data flow sequences, making them easy to write, understand, and maintain. -- Optimization opportunities. The way in which tasks are encoded permits the system to optimize their execution automatically, allowing the user to focus on semantics rather than efficiency. -- Extensibility. Users can create their own functions to do special-purpose processing.

Instead of a dry technical overview, I am going to explain the structure of this module based on its history. I consult at a company that generates customer leads primarily by having websites that attract people (e.g. lowering loan values, selling cars, buying real estate, etc.). For some reason we get more than our fair share of profane leads. For this reason I was told to write a profanity checker. For the data that I was dealing with, the profanity was most often in the email address or in the first or last name, so I naively started filtering profanity with a set of regexps for that sort of data. Note that both names and email addresses are unlike what you are reading now: they are not whitespace-separated text, but are instead labels. Therefore full support for profanity checking should work in 2 entirely different contexts: labels (email, names) and text (what you are reading). Because open-source is driven by demand and I have no need for detecting profanity in text, only label is implemented at the moment. And you know the next sentence: "patches welcome" :)

The goal of the lensfun library is to provide an open source database of photographic lenses and their characteristics. In the past there was an effort in this direction (see http://www.epaperpress.com/ptlens/), but then author decided to take the commercial route and the database froze at the last public stage. This database was used as the basement on which lensfun database grew, thanks to PTLens author which gave his permission for this, while the code was totally rewritten from scratch (and the database was converted to a totally new, XML-based format). The lensfun library not only provides a way to read the lens database and search for specific things in it, but also offers a set of algorithms for correcting images based on detailed knowledge of lens properties and calibration data. Right now lensfun is designed to correct distortion, transversal (also known as lateral) chromatic aberrations, vignetting, and colour contribution of the lens (e.g. when sometimes people says one lens gives "yellowish" images and another, say, "bluish").

Ploticus is script-driven, which makes it suitable for automated, unattended uses, or for applications that will be run again and again. Ploticus might be your choice for stylistic reasons or just because it suits the problem or application. In general, ploticus is good at making graphs like you would see in newspapers and news magazines, business publications, journals for medical and social sciences, and so on. You can also use Ploticus in combination with standard desktop tools, e.g. generate data displays using ploticus then import SVG or PNG into PowerPoint, Word, etc.) Ploticus is not a function or mathematical plotting package like gnuplot, nor would it be a good choice for applications where mathematical formulas or scientific notations are to be rendered as an integral part of the data display. Ploticus is also not intended as a "marketing" graphics package. Its goal is to display data crisply without extra decoration and distracting "dingbats" that cloud the picture. Thus there is little support for 3-D effects, gradient backgrounds, and so on. FreeBSD note: the binary is referred to as 'pl' in the source files, but is installed as 'ploticus' so as to avoid conflicts with other ports.

3[APA3A] tiny proxy 3Proxy (pronounce it as "Zaraza tiny proxy") is really tiny cross-platform (Win32&Unix) proxy servers set. It includes HTTP proxy with HTTPS and FTP support, SOCKSv4/SOCKSv4.5/SOCKSv5 proxy, POP3 proxy, TCP and UDP portmappers. You can use every proxy as a standalone program (socks, proxy, tcppm, udppm, pop3p) or use combined program (3proxy). Combined proxy additionally supports features like access control, bandwidth limiting, limiting daily/weekly/monthly traffic amount, proxy chaining, log rotation, sylog and ODBC logging, etc. It's created to be small, simple (I'd like to say secure - but it's just a beta) and yet functional. It may be compiled with Visual C or gcc. Native Win32 version included in archive and supports installation as NT/2K/XP service. Currently 3proxy is tested to work under Windows 98/NT/2000/2003/XP, FreeBSD/i386, Linux/i386, Linux/Alpha. See Release Notes and Changes for features list. 3proxy is FreeWare. It can be used under terms of GNU/GPL or under its own license (please read License Agreement). For licensing or commercial support please e-mail to 3proxy@3proxy.ru

LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification. Since version 2.8, it implements an SMO-type algorithm proposed in this paper: R.-E. Fan, P.-H. Chen, and C.-J. Lin. Working set selection using second order information for training SVM. Journal of Machine Learning Research 6, 1889-1918, 2005. You can also find a pseudo code there. Our goal is to help users from other fields to easily use SVM as a tool. LIBSVM provides a simple interface where users can easily link it with their own programs. Main features of LIBSVM include * Different SVM formulations * Efficient multi-class classification * Cross validation for model selection * Probability estimates * Weighted SVM for unbalanced data * Both C++ and Java sources * GUI demonstrating SVM classification and regression * Python, R (also Splus), MATLAB, Perl, Ruby, Weka, Common LISP and LabVIEW interfaces. C# .NET code is available. It's also included in some learning environments: YALE and PCP. * Automatic model selection which can generate contour of cross valiation accuracy.

Nux is a small, straightforward, and surprisingly effective open-source extension of the XOM XML library. Nux is geared towards versatile embedded integration and interchange, in particular for high-throughput server container environments (e.g. large-scale Peer-to-Peer messaging network infrastructures over high-bandwidth networks, scalable MOMs, etc). But its simplicity also makes it useful for client side XML query/transformation workflow pipelines. Features include: - Seamless W3C XQuery support for XOM. - Efficient and flexible pools and factories for XQueries, XSL Transforms, as well as Builders that validate against various schema languages, including W3C XML Schemas, DTDs, RELAX NG, Schematron, etc. - For simple and complex continuous queries and/or transformations over very large or infinitely long XML input, a convenient streaming path filter API combines full XQuery support with straightforward filtering. - Glue for integration with JAXB and for queries over ill-formed HTML. - All this is rock-solid, dependable, well documented, and ships in a jar file that weighs just 60 KB.

Advanced directory tree synchronisation tool (c) 2014-2016 Thomas Khyn (c) 2003-2015 Anand B Pillai Advanced directory tree synchronisation tool based on Python robocopier by Anand B Pillai Usage From the command line: dirsync <sourcedir> <targetdir> [options] From python: from dirsync import sync sync(sourcedir, targetdir, action, **options)

LIRC is a package that allows you to decode and send infra-red signals of many (but not all) commonly used remote controls. The most important part of LIRC is the lircd daemon that will decode IR signals received by the device drivers and provide the information on a socket. It will also accept commands for IR signals to be sent if the hardware supports this. The second daemon program called lircmd will connect to lircd and translate the decoded IR signals to mouse movements. You can e.g. configure X to use your remote control as an input device. The user space applications will allow you to control your computer with your remote control. You can send X events to applications, start programs and much more on just one button press. The possible applications are obvious: Infra-red mouse, remote control for your TV tuner card or CD-ROM, shutdown by remote, program your VCR and/or satellite tuner with your computer, etc.