Mar 302015

GDPC 2.0


GDPC ( Genomic Diversity and Phenotype Connection) simplifies access to genomic diversity and phenotype data, thereby encouraging reuse of this data. GDPC accomplishes this by retrieving data from one or more data sources and by allowing researchers to analyze integrated data in a standard format. GDPC provides access to genomic diversity data such as SNPs, SSRs, sequences, etc. and phenotypic data that may be collected in field, genetic, or physiological experiments.


The Buckler Lab



  • Linux /  Windows / MacOsX
  • Java




GDPC: connecting researchers with multiple integrated data sources.
Casstevens TM, Buckler ES.
Bioinformatics. 2004 Nov 1;20(16):2839-40. Epub 2004 Apr 22.

Mar 302015
TASSEL 5.0 - Association And Diversity Analyses In Plants And Animals

TASSEL 5.0 :: DESCRIPTION TASSEL (Trait Analysis by aSSociation, Evolution, and Linkage) is a software package which performs a variety of genetic analyses. The analyses include association mapping, diversity estimation and calculating linkage disequilibrium. The association analysis between genotypes and phenotypes can be performed by either a general linear model or a mixed linear model. […]

Mar 302015
SNPLINK - Multipoint Linkage analysis of Densely Distributed SNP data

SNPLINK :: DESCRIPTION SNPLINK is a Perl script that performs full genome linkage analysis of high-density single nucleotide polymorphism (SNP) marker sets. It first removes unlikely genotypes and performs parametric and non-parametric linkage analysis in a fully automated fashion. The presence of linkage disequilibrium (LD) between closely spaced SNP markers can falsely inflate linkage statistics. […]

Mar 302015
PopBio 3.0.3 - Population Biology Simulation package

PopBio 3.0.3 :: DESCRIPTION “PopBio” is a population biology simulation package. It contains components for population growth, population genetics, predator/prey interactions, and interspecific competition.The program has an extremely versatile interface that students have found very easy to use. Stochastic options allow for the design of experiments and both graphic and numerical outputs allow for export […]

Mar 292015
MiniInbred 2.1 - Calculate and Minimize Inbreeding Coefficients

MiniInbred 2.1 :: DESCRIPTION MiniInbred predicts inbreeding levels in the next generation by identifying matings that yield the lowest inbreeding level in the offspring. The inbreeding coefficients resulting from all potential matings of the current breeding animals (generation 1) are calculated, and the potential matings among the current breeding animals that yield the lowest inbreeding […]

Mar 292015
powerGWASinteraction 1.1.1 - Power Calculations for Interactions for GWAS

powerGWASinteraction 1.1.1 :: DESCRIPTION powerGWASinteraction is the code for approximate power calculations for identification of gene x gene and gene x environment interactions in genomewide association studies using a two-stage analysis. ::DEVELOPER Charles Kooperberg :: SCREENSHOTS N/A :: REQUIREMENTS Windows/Linux/MacOSX R package :: DOWNLOAD   powerGWASinteraction :: MORE INFORMATION Citation C. Kooperberg and M. LeBlanc (2008). […]

Mar 272015
dmGWAS 3.0 - Genome-wide Association Studies (GWAS) Analysis

dmGWAS 3.0 :: DESCRIPTION dmGWAS is designed to identify significant protein-protein interaction (PPI) modules and, from which, the candidate genes for complex diseases by an integrative analysis of GWAS dataset(s) and PPI network. ::DEVELOPER Bioinformatics and Systems Medicine Laboratory, Vanderbilt University :: SCREENSHOTS N/A :: REQUIREMENTS Linux  / WIndows R package :: DOWNLOAD  dmGWAS :: MORE INFORMATION […]

Mar 272015
GLECLUBS / eGLECLUBS - extended / Predicting Cis-regulatory Binding Sites in Prokaryotes

GLECLUBS / eGLECLUBS :: DESCRIPTION GLECLUBS (Globle Ensemble Clusters of Binding Sites) is an algorithm for predicting cis-regulatory binding sites in prokaryotes eGLECLUBS is an extended version of GLECLUBS for simultaneously predicting binding sites in a group of closely related prokaryotic genomes ::DEVELOPER Dr. Su’s lab at the University of North Carolina at Charlotte. :: […]

Mar 272015
MotifClick - Motif Finding program

MotifClick :: DESCRIPTION MotifClick is a motif-finding tools ::DEVELOPER Dr. Su’s lab at the University of North Carolina at Charlotte. :: SCREENSHOTS N/A :: REQUIREMENTS Linux /Windows / MacOsX C++ Compiler :: DOWNLOAD  MotifClick :: MORE INFORMATION Citation BMC Bioinformatics. 2011 Jun 16;12:238. doi: 10.1186/1471-2105-12-238. MotifClick: prediction of cis-regulatory binding sites via merging cliques. Zhang […]

Mar 272015
TruHmm - TRanscription Unit Assembly by a Hidden Markov model

TruHmm :: DESCRIPTION TruHmm is a reference based transcriptome assembler for prokaryotes, and is suitable for assembling transcripts for directional RNA-seq library. ::DEVELOPER Dr. Su’s lab at the University of North Carolina at Charlotte. :: SCREENSHOTS N/A :: REQUIREMENTS Linux /Windows Perl / C++ :: DOWNLOAD  TruHmm :: MORE INFORMATION Citation BMC Genomics. 2013 Jul […]