Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
Desktop search application
DocFetcher is an Open Source desktop search application: It allows you to search the contents of files on your computer. — You can think of it as Google for your local files. The application runs on Windows, Linux and Mac OS X.
One hundred command line tools in a small and portable binary.
Replace text in files, search in files using expressions, stream text editor, instant command line ftp and http server, send folder via network, copy folder excluding sub folders and files, find duplicate files, run a command on all files of a folder, split and join large files, make md5 checksum lists of files, remove tab characters, convert CR/LF, list newest or biggest files of a folder, compare folders, treesize, show first or last lines of a file, find filenames fast using index files, rename many files using expressions, copy part of a file, change times of a file, delete files in selected sub folders, set file time from filename, print colored text to terminal, convert csv to tab separated, download files from web, send http or udp requests, print tcp or udp traffic, create hexdump of files, join many text files into one, list nested .zip .tar .tar.gz .tar.bz2 archive contents. Fully portable, for USB stick, without installation. For Windows, Linux and Mac OS/X.
deletes junk files to free disk space and improve privacy
BleachBit frees disk space and maintains privacy. Cleans cache, Internet history, temporary files, logs, cookies, Firefox, Google Chrome, Flash, Windows, Linux, and more. Downloads are at www.bleachbit.org and source code is at GitHub.
Search and replace operations on file content accross multiple files. Recursive operations within entire directory trees. FAR comes with support for regular expressions (regex) over multiple lines, automatic backup and various character encodings. Run grep like extractions to condense or rearrange sources, or perform bulk file renaming.
CLucene is a C++ port of Lucene: the high-performance, full-featured text search engine written in Java. CLucene is faster than lucene as it is written in C++.
An open source search engine with RESTFul API and crawlers
OpenSearchServer is a powerful, enterprise-class, search engine program. Using the web user interface, the crawlers (web, file, database, etc.) and the client libraries (REST/API , Ruby, Rails, Node.js, PHP, Perl) you will be able to integrate quickly and easily advanced full-text search capabilities in your application: Full-text with basic semantic, join queries, boolean queries, facet and filter, document (PDF, Office, etc.) indexation, web scrapping,etc. OpenSearchServer runs on Windows and Linux/Unix/BSD.
Powerful desktop search app for Windows, Linux and Mac
Power searching on your desktop without the pain. Perform powerful desktop searches without having to index your system using regular expressions. Graphical equivalent to find/grep. Available for Windows (JAVA) and Linux (Gnome & KDE) and easy to translate into your locale.
phpMorphy is morphological analyzer library written in pure PHP. Currently supports Russian, English and German languages.
Aperture is a Java framework for extracting and querying full-text content and metadata from various information systems (file systems, web sites, mail boxes, ...) and the file formats (documents, images, ...) occurring in these systems.
Launchy is a free utility designed to help you forget about your start menu, your desktop icons, and your file manager. Launchy indexes and launches your applications, documents, project files, folders, and bookmarks with just a few keystrokes!
disk manager is a CD/DVD archiving tool. It storys the directory contents of any media so you can search it later. Its also designed as file explorer which makes it easy to find big files. Windows Version supports native file context menus.
GDuplicateFinder - A FREE Groovy way to find file duplicates!
Unlike other duplicate finders such as Easy Duplicate File Finder, Auslogics Duplicate File Finder, MindGems Fast Duplicate File Finder, Duplicate Cleaner, DupFiles and others, GDuplicateFinder is a FREE cross-platform application, with the ability to search among not just local files, but files on the network, such as a Windows or a Linux share using VFS library. Taking advantage of Groovy facilities and GPars power to process in parallel, GDuplicateFinder will help you get rid of those duplicates you always wanted to dispose in an easy and friendly way. Looking for translators to translate the app! If you'd like to help me, just send me an e-mail to firstname.lastname@example.org. Thanks in advance If you want to help me continue improving this app, donate some money through paypal! https://www.paypal.com/cgi-bin/webscr?cmd=_s-xclick&hosted_button_id=fezuqqg9t6j6y
A small application for listing the contents(files/folders/extensions) of a folder. The results includes file name length/full path length/maximum extensions. It supports exporting a report in .txt/.csv format with fully customizable contents.
An advanced Java file/class finder with support for searching inside zip|war|ear|jar archives or finding text inside pdf|doc|ppt|UTF-8 files.
Tagging system for local files
Reggata is a tagging system for managing local files on a computer. Use it for organizing your huge collections of music, ebooks and photos (or any other files) with tags. TESTERS NEEDED! Help the project: submit BUGS and request NEW FEATURES here https://github.com/vlkv/reggata/issues Send me your FEEDBACK email@example.com !!!
Java application using tree map algorithms to visualise disc space usage. Lets find forgotten large "space-eaters" files in an easy way.
Find, select, delete empty folders. Use the ignore list and others.
Empty Directories Finder expires empty directories and allows you to conveniently select the required directories before deleting.
OpenEphyra is an open framework for question answering (QA). It retrieves answers to natural language questions from the Web and other sources. Visit http://www.ephyra.info/ for more details and information on joining this open research initiative.
zfind is a fast file search utility/API for searching within archives
Many times, developers (or even, normal users) run into an issue of searching for a resource that is inside a zip. Worse, that resource is inside a zip which is itself inside ANOTHER zip (i.e. nested archive). Possibly you need to verify whether a particular resource is present in an ear or you want to know part of a file name but don't know which zip/jar on your hard disk contains that class file. zfind solves this problem. zfind is very fast and it works on most common archive/compress files. Apart from GUI and command line, it also provides API support which let's you use it in your java code as a 3rd party library. Thanks for using, and if you find any bug, do post a ticket or discussion topic. I can't fix anything if I don't know the problem :) **Check Wiki for USAGE details
JarFinder is a java swing based utility application, which helps in locating a jar file out of a given set of jar files. It takes a Class name/Fully qualified class name as search parameter and finds the jar for the same.
Pdfgrep is a tool to search text in PDF files. It works similar to grep.
Puggle is a graphical desktop search engine written exclusively in Java. It provides full text and metadata search over files, folders, music, photos, web pages and more that are stored locally on your computer.
PHP Security Scanner is a tool written in PHP intended to search PHP code for vulnarabilities. MySQL DB stores patterns to search for as well as the results from the search. The tool can scan any directory on the file system.
The MARKet for Open Source
MARKOS will realize the prototype of a service and an interactive application providing an integrated view on the Open Source projects available the on web, focusing on functional, structural and licenses aspects of software code.