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If you manage phylogenetic data, Bio::NEXUS can make your life easier with a library and ready-made tools to manipulate and visualize NEXUS files (see http://www.molevol.org/nexplorer and http://search.cpan.org/dist/Bio-NEXUS/doc/Tutorial.pod).
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).
A small command line tool to process streams of numbers and spit out the running total, bin the results or merge duplicates. Supports arbitrary precision numbers. ocdf is named for the cumulative distribution function in probability.
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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!
FNA is a command line tool for creating and analyzing financial networks with concepts developed in social network analysis and network science. NOTE: the project has been moved to http://code.google.com/p/financial-network-analyzer/
This is a simple command line tool to customize CP2103 USB to UART bridge controllers in home-grown hardware. VID, PID, product name string, serial number string, and release version of the device can be changed next to GPIO port modes.
bc2ld is a command line tool to translate molecular database files from BASECOL (obs. of Paris) to LAMDA format (Leiden University). This command line tool has academic use purposes.
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This is a Python interface for reading and writing Magellan GPS unit map files. There is also a command line tool for creating GPS maps from OpenStreetMap data.
This is a small and fast library and command-line tool for manipulation of logic/boolean-algebra expressions, including proofing and simplification. A front-end using tigcc for Texas Instruments calculators is planned, too.
IntiMap is a convenience tool to run the MS-DOS command-line tool MapPop for selective genotyping. It adds facilities to prepare genotyping data files, manage genotype sets and visualize mapping results (genetic marker maps).
Command line tool to generate Gcode for CNC applications from DXF files. Originally written for 2-axis machines such as foam cutters, it now supports 3-axis machines.
van-der-Waals-Equation Calculator (vdw_calc) is a small command line tool to solve the van-der-waals-equation and calculate coefficients for different gases.
SymDiff is a little command line tool for symbolic differentiation and expression evaluation. Furthermore, the code can be used for the symbolical implementation of certain mathematical algorithms that require derivatives.
Racron is a command line tool that calculates the dynamic response of
systems with a single degree of freedom (SDOF), due to external force
or earthquake excitation. It supports linear & bilinear systems and
utilizes various time-stepping methods.
A command line tool that allows a semi-automated scientific articles management. It assumes an existence of a directory of a specific format in the file system. The tool interprets the data stored in the directory (called a repository), extend it via the usage of some automatic tools such as pdftotext, and search the text as well as some metadata.
OC-CLI gives you a stable command surface for database maintenance, extensions, cache work, catalog operations, orders, and admin-user management. Runtime-backed commands target real OpenCart 3.x installations. DB-native commands can run with direct credentials.