:: DESCRIPTION
CONTOUR is a systematic tracking of dysregulated modules identifies novel genes in cancer
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Srihari S & Ragan MA (2013)
Systematic tracking of dysregulated modules identifies novel genes in cancer,
Bioinformatics 29(12):1553–1561. doi: 10.1093/bioinformatics/btt191
:: DESCRIPTION
The PhyloMap can generate elegant visualizations for large sequence data sets up to thousands of taxon require only a relatively short computation time. It can give you an overview of your entire data set, and automatically select a small number of sequences which are evenly sampled across your data set. You can build a phylogenetic tree using the sampling sequences and use it as a reference data set for further studies. The PhyloMap also shows you the relationships between the sampled data set with the entire data set.
::DEVELOPER
Jiajie Zhang (zhangjiajie@biochem.uni-luebeck.de)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2011 Jun 20;12:248. doi: 10.1186/1471-2105-12-248.
PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome.
Zhang J1, Mamlouk AM, Martinetz T, Chang S, Wang J, Hilgenfeld R.
:: DESCRIPTION
SIMLAPLOT is a software for visualizing different ways in which continuous covariates may influence the genotype-specific risk for complex human diseases. The purpose of our study was to examine continuous covariates in the Genetic Analysis Workshop 15 simulated data set using our novel graphical display tool, with knowledge of the answers. The generated plots provide information about genetic models for the simulated continuous covariates and may help identify the single-nucleotide polymorphisms associated with the underlying quantitative trait loci.
::DEVELOPER
Duke Molecular Physiology Institute
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Xuejun Qin,et al
Visualizing genotype × phenotype relationships in the GAW15 simulated data
BMC Proc. 2007; 1(Suppl 1): S132.
:: DESCRIPTION
GNC is a Java-based software tool for analyzing gene networks coherence using direct and indirect relationships.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Gene network coherence based on prior knowledge using direct and indirect relationships.
Gómez-Vela F, Lagares JA, Díaz-Díaz N.
Comput Biol Chem. 2015 Jun;56:142-51. doi: 10.1016/j.compbiolchem.2015.03.002.
:: DESCRIPTION
RelCheck is a software for verifying relationships between all pairs of individuals in a linkage study
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Broman, Weber (1998),
“Estimation of pairwise relationships in the presence of genotyping errors” (letter),
American Journal of Human Genetics, 63(5):1563-1564.
:: DESCRIPTION
relativeFinder is a program for checking relationships between pairs of individuals. There are many excellent programs that carry out similar tasks. Some of the unique features in relativeFinder are the batch mode options, that allow large jobs to be divided into many smaller jobs (suitable for deployment on a compute cluster environment), and the flexibility of the underlying Merlin engine, which allows relative finder to handle large pedigrees and consider a variety of alternate relationships — including potential relationships specified by the user on the fly!
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
ML-Relate is a computer program that calculates maximum likelihood estimates of relatedness and relationship. ML-Relate is designed for microsatellite data, and can accommodate null alleles. It uses simulation to perform two types of hypothesis tests.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kalinowski ST, AP Wagner, ML Taper (2006).
ML-Relate: a computer program for maximum likelihood estimation of relatedness and relationship.
Molecular Ecology Notes 6:576-579.
:: DESCRIPTION
CompClust is a python package written using the pyMLX and IPlot APIs. It provides software tools to explore and quantify relationships between clustering results. Its development has been largely built around needs of microarray data analysis but could be easily used in other domains.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Nucleic Acids Res. 2005 May 10;33(8):2580-94. Print 2005.
A mathematical and computational framework for quantitative comparison and integration of large-scale gene expression data.
Hart CE, Sharenbroich L, Bornstein BJ, Trout D, King B, Mjolsness E, Wold BJ.
:: DESCRIPTION
RELPAIR is a FORTRAN 77 program that infers the relationships of pairs of individuals based on genetic marker data, either within families or across an entire sample.
::DEVELOPER
the Center for Statistical Genetics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Epstein, M.P., Duren, W.L., and Boehnke, M. (2000)
Improved inference of relationships for pairs of individuals.
American Journal of Human Genetics 67:1219-1231.
