Gene

GATA is a graphic alignment tool for comparative sequence analysis. It makes use of BLAST to graphically align two DNA sequences, creating box- line- box representations of window scored local alignments. GATA also displays extensive GFF gene annotation. Platforms: Windows, Mac, Linux

An object oriented library of an Genetic Algorithm, implemented in Java. Clear separation of the several concepts of the algorithm, e.g. Gene, Chromosome, Genotype, Phenotype, Population and Fitness Function. The fitness calculation is parallelized. Platforms: Windows, Mac, Linux

LineageEvolver is a simulation system for molecular evolution. Sequence evolution is simulated using modular processes such as substitutions, gene duplication/death, horizontal gene transfer, and more. Platforms: Windows, Mac, Linux

Microarray Explorer (MAExplorer) is a Java microarray data-mining bioinformatics program. It includes data management, graphics, statistics, clustering, reports, gene data-filtering, user written MAEPlugins, documentation, tutorials, demo data. Platforms: Windows, Mac, Solaris, Linux

Osprey is a software platform for visualization of complex interaction networks. Osprey builds data-rich graphical represetations from Gene Ontology (GO) annotated interactions maintained by the BioGRID. Platforms: Windows, Mac, Solaris, Linux

PanOCT, Pan-genome Ortholog Clustering Tool, is a program written in PERL for pan-genomic analysis of closely related prokaryotic species or strains. Unlike traditional graph-based ortholog detection programs, it uses micro synteny or conserved gene neighborhood (CGN) in addition to homology to... Platforms: Mac, Linux

A Tool for Retrieval, Visualization and Analysis of biological Pathways. Import a Gene or Protein Set from any Excel file. Automatically find signaling Pathways from KEGG. Integrate your Data in Seconds with a live interactive Force-directed Layout. Platforms: Windows, Mac

QTL Reaper analyzes data from progeny of a genetic cross in experimental plants or animals. It seeks the location of genes that affect a heritable trait, and it is specially designed for analysis of gene expression measurements. Platforms: Mac, Linux

Syntainia is an innovative tool for visualization of multiple genomes. It presents a simple and intuitive user interface to view and manipulate relationships between groups of genes. With a clearer gene visualization, it is easier for the researcher to identify synteny conservation among multiple... Platforms: Mac

This script provides a class called LineIterator that iterates over every line in a list of files, performing the basic functionality as fileinput module in the standard library (which mimics Perl's operator). Basically acts as a simple and methodical way to iterate over every line in a list of... Platforms: Windows, Mac, *nix, Python, BSD Solaris

HapCluster is a software package for linkage disequilibrium mapping.It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. Platforms: C and C plus plus

PID controller has been extensively used in the industrial world. But in this controller it is difficult to tune the PID gains.We apply the genetic algorithm(GA) to tune the PID gains. The GA is agorithm using the biotic; gene the biotic; genetics. Platforms: Matlab

This package is the mRMR (minimum-redundancy maximum-relevancy) feature selection method in (Peng et al, 2005 and Ding & Peng, 2005, 2003), whose better performance over the conventional top-ranking method has been demonstrated on a number of data sets in recent publications. This version uses... Platforms: Matlab

The CMVE toolbox estimates missing values by using correlation structure of the data. The software can be used to impute missing values in any correlated data especally microarray gene expression data. The imputation performance of the software has proven significant affect on gene regulatory... Platforms: Matlab

MATLAB Builder for COM enables you to deploy MATLAB algorithms as COM objects, which can be used on any web server on a Microsoft operating system. The MATLAB based COM object will handle your technical computing, while integrating with a front-end web application built using industry-standard... Platforms: Matlab

Reverse transcription(RT) followed by PCR is a powerful tool for the detection and quantification of mRNA. It is the most sensitive method for the detection and quantification of gene expression levels, in particular for low abundance mRNA.The relative quantification is based on the expression... Platforms: Matlab

Dynamic Bayesian networks (DBN) are widely applied in modeling various biological networks, including the gene regulatory network. Due to several NP-hardness results on learning static Bayesian network, most methods for learning DBN are heuristic, that employ either local search such as greedy... Platforms: Matlab

Blast2GO?*A* is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Main Application Features are: Easy start up and low maintenance. Make sure you have JAVA, download Blast2GO from this site and start using the application. Updates are... Platforms: Mac

The Synonym and Global Translator is a Gaggle Enabled Java program that enables a user to translate between different gene identifiers and find orthologous genes for a number of different species through the use of the BioNetBuilder database server. It is free to use, but is no longer actively... Platforms: Mac

JAtlasViewer is a program for selecting and viewing virtual sections from woolz format 3D images. Since any arbitrary section plane can be chosen, it can be used to explore the internal space of these 3D images. Examples of suitable format 3D images include the EMAP mouse embryo models, the... Platforms: Mac