RSS 154 projects tagged "Bioinformatics"

Download Website Updated 15 Mar 2002 BioJava

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Pop 156.80
Vit 2.38

BioJava aims to provide a comprehensive set of Java components for the rapid development of applications in Bioinformatics. It contains interfaces for representing Sequences, Features, and other important bioinformatics concepts. It can also read and write sequence data in a variety of common formats and communicate with Ensembl databases and with DAS and BioCorba servers.

Download Website Updated 27 Sep 2009 Bioperl

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Pop 98.07
Vit 8.04

Bioperl is set of Perl Modules for bioinformatics. It contains objects for Sequences, features on Sequences, and other important bioinformatics attributes.

No download Website Updated 15 Aug 2001 Ensembl

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Pop 18.06
Vit 1.83

Ensembl is an open source project to create and automatically maintain annotations on DNA sequence.

Download Website Updated 06 Jun 2001 Genpak

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Pop 38.57
Vit 2.96

Genpak is a small set of utilities designated to process DNA, RNA, and protein sequences in a very Un*x-like manner. This way, Genpak programs can be combined using pipes and redirections, as well as easily incorporated into CGI scripts. The utilities include a program for calculating GC content, Tm, translating DNA/RNA sequences into protein sequences, quick sequence retrieval, random sequence generation, and finding promoter sequences using a Hertz matrix.

Download Website Updated 22 Sep 2006 JChemPaint

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Pop 172.07
Vit 9.11

JChemPaint is a program for drawing 2D chemical structures like those found in most chemistry textbooks.

Download Website Updated 30 Jan 2001 Mavric

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Pop 12.37
Vit 1.00

Mavric is a python module/application that aims to be a user-friendly tool for manipulating phylogenetic trees on *NIX-like systems running X Windows. As such, it complements other phylogeny programs that currently lack a nice graphical interface.

Download Website Updated 17 Apr 2009 R

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Pop 463.65
Vit 12.83

R is a language and environment for statistical computing and graphics. It is similar to S, which was developed at Bell Laboratories by John Chambers et al. It provides a wide variety of statistical and graphical techniques (linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc.). R is designed as a true computer language with control-flow constructions for iteration and alternation, and it allows users to add additional functionality by defining new functions. For computationally intensive tasks, Fortran and C code can be linked and called at run time.

Download Website Updated 14 Feb 2012 VMD

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Pop 129.52
Vit 13.42

VMD (Visual Molecular Dynamics) is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. VMD uses OpenGL and OpenGL Programmable Shading Language for high performance rendering of large structures.

Download Website Updated 30 Jan 2001 WEKA

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Pop 82.69
Vit 1.00

Weka is a collection of machine learning algorithms for solving real-world data mining problems. It is written in Java and runs on almost any platform. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka is also well-suited for developing new machine learning schemes. The development version contains a GUI with visualization tools and direct database access.

Download Website Updated 06 Jun 2001 Arka

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Pop 14.11
Vit 3.20

Arka provides a nice GUI for the gp package of command-line utilities for manipulation and display of DNA/RNA/protein sequences, the WU-BLAST and FASTA program families, and additional graphical tools for various aspects of sequence analysis (e.g., GC plots and 3D graphs). It provides editable and saveable windows for standard input, output and error, and a dialog for any command-line program with specifications in a configuration file.

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Software that converts data into something meaningful and interpretable.