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Diva is a command-line tool for dispersal-vicariance analysis, a simple method for inferring the distributional history of organisms (Ronquist, F. 1997. Systematic Biology 46:193-201).
JFtpSync is for uploading web content to a server via FTP. It is designed to do FTP uploading only, and do it well, offering recursive uploading of content filtered by file type. It is primarily a command-line tool but there is a Java GUI as well.
CLIG - CommandLine Interface Generator Clig is a code generator for several programming languages that allows you easy creation of commandline parsers. Including a GUI and CommandLine tool.
RtMidiRouter is a small but powerful commandline tool which allows you to route, manipulate and create MIDI messages. For reliable realtime performance RtMidiRouter is based on RtMidi. It is controllable via commandline and network (OSC).
SubtitleGet is a command-line tool written in Python, that I am creating in my spare time. It's main purpose is to search, download and/or upload subtitles using Opensubtitles.org fantastic site.
jTCPfwd started as a simple Java commandline tool to forward TCP ports. Lots of other features are added, for example for forwarding TCP connections over reverse TCP connections, UDP/HTTP tunnelling or writing files to a network share.
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Commandline tool for syncronize heterogeneous databases. Work via QT4 drivers (Drivers for SQLite, QDBC, Firebird are included. Drivers for IBase, DB2, Postgeress, Mysql may be compilled by Qt4 (4.7.0 for 0.0.4)))
brn is a Perl-based command-line tool designed to ease the task of bulk renaming a large number of files. Started as a fork of the standard perl 'rename' tool, this project has since mutated significantly and is still undergoing rapid flux.
Pieman is a command-line tool for managing personal information such as appointments, contacts, and tasks as well as other data such as notes and rc files. It is a portable pure-perl tool inspired by abook, devtodo, mutt, and pal, among others.
SplitPDF -SplitPDF.jar- is a ‘command-line driven’ Java-program, it splits a PDF-file by bookmarks into separated PDF’s. The bookmark is used as title for the newly created PDF. Extremely usefull and fast in a batch processing environment.
The SBML ODE Solver is a command-line tool and programming library (ISO/ANSI C) for construction and numerical integration of an ODE system, derived from an SBML based description of a biochemical reaction network.
Development has moved to https://github.com/raim/SBML_odeSolver . Please download the latest version from there!
KMLTool (better name wanted) is a commandline tool written in java, mainly designed to automate the process of converting kismets .gpsxml/.netxml files into google earth's KML files, with some features i used to miss in other programs for this job.
ODic stands for "Options Dictionary" and aims at creating standards for easier commandline tool creation. At the moment it is focused on the 'odic' python module including new design patterns for python main functions.
hscratch is a simple command-line tool to produce scratch sounds from a given phonogramme offline coded in Haskell. Currently, it lacks all that command-line sugar like '-v' and '-h'. Working prototype, still to be developed and improved.
Let's you synchronize related scheduled jobs, which execute across many different machines. Instead of adding time padding between jobs (which can fail), use this utility. Please feel free to add more functions!
A tool that can extract data from the Calibre SQLite database, including a commandline tool that generates OPDS catalogs. In everyone's words, it takes the metadata out of Calibre, and generates catalogs for Stanza, Aldiko and web browsers.
A small command-line tool for converting AtariST images (.neo, .pi1, .pi2, .pi3) to gifs (using gd).
Please note that you may find the project "RECOIL" at SF, which supports far more formats.