Chromosome

Calculates derivative log ratio spread for copy number log ratio data per chromosome and overall. This is the standard deviation of the differences between adjacent points divided by the square root of 2. Missing values are skipped. Assumes: * Samples are rows of the spreadsheet * A marker...

Diversity Maps was specially developed as a data visualization utility for plant geneticists and breeders. Diversity Maps is a Perl-based tool that can generate publication-quality, vector-based chromosome maps displaying differences in marker states between individuals.

The Genetic Algorithm Utility Library (or, GAUL for short) is a flexible programming library designed to aid in the development of applications that use genetic, or evolutionary, algorithms. It provides data structures and functions for handling and manipulation of the data required for serial...


Platforms: C and C plus plus

This script creates a binary spreadsheet to indicate if there exists a rare variant in the window centered about the current marker. At chromosome edges, the maximum number of markers up to the window size is used without running into the next chromosome.


Platforms: Mac

This script calculates thresholds for the top and bottom percentiles of log ratio data, as specified by the user, for the purpose of winsorizing * replacing extreme log ratio values with the calculated thresholds. Winsorizing data prevents segmentation algorithms from being driven by outlier...


Platforms: Mac

SAMMate, a Graphical User Interface (GUI) RNA-seq analysis pipeline, allows biomedical researchers to quickly process SAM/BAM files and is compatible with both single-end and paired-end sequencing technologies. SAMMate automates some of more standard procedures in RNA-seq analysis. Features:...


Platforms: Mac

JGAP (pronounced "jay-gap") is a genetic algorithms component written in the form of a Java package. JGAP project provides basic genetic mechanisms that can be easily used to apply evolutionary principles to problem solutions. The ground is laid for introducing Genetic Programming to JGAP in the...


Platforms: *nix

Evocosm is a C++ Framework for Evolutionary Computing library. Evocosm is a set of classes that abstract the fundamental components of an evolutionary algorithm. Ill list the components here with a bit of introduction; you can review the details of the classes by downloading the code archives...


Platforms: *nix

Jenetics is a Java based object oriented library of an Genetic Algorithm. The library offers a clear separation of the several concepts of the algorithm, e.g. Gene, Chromosome, Genotype, Phenotype, Population and FitnessFunction. for WindowsAll


Platforms: Windows

The Gene Expression Programming Framework in Java.It separates the process of evolution from the process of interpretation of the chromosome, allowing the use of various schemes in the chromosome.


Platforms: Windows, Mac, Linux

Audio Analysis/Resynthesis the way Darwin would have done it if he were only into computer music. Using a genetic algorithm to evolve a sinusoidal/noise based sound model, create variations as the audio chromosome of a sound's family tree progresses.


Platforms: Mac

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

Diversity Maps is a data visualization tool for plant geneticists and breeders. It generates publication-quality, vector-based chromosome maps displaying differences in marker states between individuals. Features Displays haplotype similarity by color; Sorts accessions automatically to...


Platforms: *nix