RSS 44 projects tagged "Bioinformatics"

Download Website Updated 09 Jul 2009 libfid

Pop 26.61
Vit 1.43

The Full-text Index Data structure library, libfid for short, is a portable software library for accessing indexed data through a simple C interface. It implements, among others, functions for reading indexed data from files, and for performing common operations such as fast string matching. Easy alphabet handling for mapping between printable and binary alphabets is integrated from the ground up. Currently, the enhanced suffix array is the only full-text index data structure supported. A very simplistic program for constructing enhanced suffix arrays is included.

Download Website Updated 20 May 2008 ParseGenBank

Pop 10.00
Vit 1.00

ParseGenBank is a minimalistic, incremental, event-driven GenBank Flat File Format parser. It aims to efficiently produce events for keywords, features, qualifiers, and coding data. It does not attempt to parse the contents of feature or qualifier data, but provides a framework on which such a system can be built.

Download Website Updated 28 Jul 2012 NCBI C++ Toolkit

Pop 49.07
Vit 5.07

The NCBI C++ Toolkit provides portable libraries and applications for assisting genetic science. These include libraries for networking, SQL and BerkeleyDB access, CGI and HTML handling, ASN.1 and XML handling, sequence alignment engines, sequence retrieval engines, BLAST database engines, FLTK and OpenGL graphics toolkits, and basic system utilities.

Download Website Updated 19 Nov 2008 Java Machine Learning Library

Pop 39.95
Vit 1.91

The Java Machine Learning Library is a set of reference implementations of machine learning algorithms. These algorithms are well documented, both in the source code as on the documentation site. Along with real machine learning algorithms, many supporting algorithms are provided: distance measures, evaluation criteria, data sets for validation purposes, and some sample code.

Download Website Updated 24 May 2010 OBSearch

Pop 36.33
Vit 2.92

OBSearch is a distributed similarity search index. It can (for example) match programs and help to detect Open Source/Libre license violations, find music that sounds like Sisters of Mercy, or match huge vectors of randomly generated integers just for fun.

Download Website Updated 21 Mar 2012 CGAL

Pop 109.20
Vit 3.62

CGAL, the Computational Geometry Algorithms Library, is a large C++ library of geometric data structures and algorithms such as Delaunay triangulations, mesh generation, Boolean operations on polygons, and various geometry processing algorithms. CGAL is used in various areas: computer graphics, scientific visualization, computer aided design and modeling, geographic information systems, molecular biology, medical imaging, robotics and motion planning, and numerical methods.

Download Website Updated 27 Sep 2007 Fast Genetic Algorithm

Pop 122.31
Vit 4.56

FGA (Fast Genetic Algorithm) is a simple yet powerful implementation of genetic algorithms. The library provides many variants of crossover and selection procedures, and a parallel version of the algorithm is included.

No download Website Updated 27 Aug 2006 PROMPT

Pop 10.25
Vit 1.00

PROMPT is a system for retrieval, analysis, mapping and comparison of protein sets. It allows easy mapping of different types of sequence identifiers, automatic data retrieval and integration, many analysis and comparison algorithms, and a full-featured GUI application. Exhaustive statistical tests are conducted automatically in appropriate cases, but can be performed manually. All analysis results can be viewed or visualized and exported in various formats. All methods can be used in your own Java code or with beanshell scripting in your own scripts, a pipeline, or grid systems.

No download Website Updated 04 Jul 2006 MyCGR

Pop 17.86
Vit 1.00

MyCGR implements the research of the thesis of Peggy Cénac regarding the use of CGR (Chaos Game Representation) to build a new family of tests for the structure of sequences. It can empirically check the level and power of the tests and apply them on DNA sequences. It can generalize the dinucleotide abundance profile to a CGR-based relative abundance profile and use this profile on DNA sequences to build taxonomy trees and to define CGR-trees.

No download Website Updated 20 Jun 2006 JColorGrid

Pop 26.72
Vit 1.75

JColorGrid is an application for graphical data exploration and the rendering of colorgrids, a generalization of the popular heat-map representation. The software exists as a command-line application, a graphical viewer, and an API for development.


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Berkeley Yacc

A high-quality yacc variant.


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A designer’s program for describing parts of the building.