:: DESCRIPTION
SweepFinder is a program used to detect the location of a selective sweep based on SNP data. It will also estimate the frequency spectrum of observed SNP data in the presence of missing data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Nielsen et al. 2005.
Genomic scans for selective sweeps using SNP data.
Genome Research 1566-1575.
:: DESCRIPTION
GMM (Gaussian Mixture Model) detects copy number variation from the distribution of copy number ratios. From the data, it will fit one component for each of the following copy number states: deletion, copy-neutral, 1 and 2 additional copy; with a constraint on the difference between the mixture means. Then for a given individual, it will determine the probabilities for each copy number state and compute the expected copy number (dosage).
::DEVELOPER
Computational Biology Group ,Department of Medical Genetics, University of Lausanne
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
PedAgree detects autosomal marker incompatibilities. PedAgree needs only pedigree file and doesn’t need locus file. The pedigree file have a very strict format because PedAgree need to distinguish markers from other variables.
::DEVELOPER
Christine Couiilault (kristin.c@free.fr)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
HapForest implements a forest-based approach to accommodate the haplotype uncertainties and variable importance to sort out significant haplotypes and their interactions in genomewide case-control association studies.
::DEVELOPER
The Collaborative Center for Statistics in Science(C2S2)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
X. Chen, C.-T. Liu, M. Zhang and H.P. Zhang.
A forest-based approach to identifying gene and gene-gene interactions,
PNAS, 104: 19199–19203, 2007.
:: DESCRIPTION
SegSeq is an algorithm to identify chromosomal breakpoints using massively parallel sequence data
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Nat Methods. 2009 Jan;6(1):99-103. Epub 2008 Nov 30.
High-resolution mapping of copy-number alterations with massively parallel sequencing.
Chiang DY, Getz G, Jaffe DB, O’Kelly MJ, Zhao X, Carter SL, Russ C, Nusbaum C, Meyerson M, Lander ES.
:: DESCRIPTION
DIVERGE is designed to detect functional divergence between member genes of a protein family, based on (site-specific) shifted evolutionary rates after gene duplication or speciation. Posterior analysis results in a site-specific profile for predicting important amino acid residues that are responsible for functional divergence. Moreover, when the 3D protein structure is available, these predicted sites can be mapped to the 3D structure viewer to explore its structure basis.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Gu, X. (1999)
Statistical methods for testing functional divergence after gene duplication.
Molecular Biology and Evolution 16:1664-1674.
:: DESCRIPTION
EPISTACY is a SAS program designed to test all possible two-locus combinations for epistatic (interaction) effects on a quantitative trait using QTL-mapping data sets.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Holland (1998),
“EPISTACY: A SAS program for detecting two-locus epistatic interactions using genetic marker information“,
Journal of Heredity, 89:374-375.
:: DESCRIPTION
HapBound-GC and SHRUB-GC respectively compute lower and upper bounds on the minimum combined number of crossover and gene-conversion recombinations. SHRUB-GC constructs a graphical representation of evolutionary history involving coalescent, mutation, crossover and gene-conversion events.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Song, Y.S., Ding, Z., Gusfield, D., Langley, C.H., and Wu, Y.
Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences
Lecture Notes in Computer Science 3909, (2006) 231-245.”
:: DESCRIPTION
The blockbuster tool automatically assigns reads to blocks and gives a unique chance to actually see the different origins where the short reads come from.
::DEVELOPER
the Hoffmann Junior Research Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Langenberger D, Bermudez-Santana C, Hertel J, Hoffmann S, Khaitovitch P, Stadler PF:
“Evidence for Human microRNA-Offset RNAs in Small RNA Sequencing Data“,
Bioinformatics (2009) vol. 25 (18) pp. 2298-301
:: DESCRIPTION
EVE (External Variance Estimation) is an software to detect differentially expressed genes using microarray data.You can download an R-script that works for data from the Affymetrix ATH1 GeneChip® microarray.
::DEVELOPER
Gruissem laboratory at the Institute of Plant Sciences
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wille, A., Gruissem, W., Bühlmann, P., Hennig, L. (2007)
EVE – External Variance Estimation increases statistical power for detecting differentially expressed genes.
Plant J 52, 561-569
