:: DESCRIPTION
EM is a software to estimate genetic distances and chiasma distribution for human UPD and trisomy data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Am J Hum Genet. 2001 Dec;69(6):1255-65. Epub 2001 Nov 5.
Multipoint genetic mapping with trisomy data.
Li J, Sherman SL, Lamb N, Zhao H.
:: DESCRIPTION
PCR Analyzer is a software to estimate the initial amount of amplicon using a simplified mechanistic model based on chemical reactions in the annealing step of the PCR.
::DEVELOPER
National Institute of Environmental Health Sciences , National Institute of Health
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Marjo V Smith , Chris R Miller, Michael Kohn, Nigel J Walker and Chris J Portier
Absolute estimation of initial concentrations of amplicon in a real-time RT-PCR process
BMC Bioinformatics 2007, 8:409doi:10.1186/1471-2105-8-409
:: DESCRIPTION
EH is a program to test and estimate linkage disequilibrium between different markers or between a disease locus and markers. This is an updated version in which the previous “disease” (case-control) option has been deleted (but see below how to work with case-control data).
::DEVELOPER
Lab of Statistical Genetics, Rockefeller University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
References
Marchini J et al (2006) A comparison of phasing algorithms for trios and unrelated individuals. Am J Hum Genet 78, 437-450
Xie X, Ott J (1993) Testing linkage disequilibrium between a disease gene and marker loci. Am J Hum Genet 53, 1107 (abstract)
Terwilliger J, Ott J (1994) Handbook of Human Genetic Linkage. Johns Hopkins University Press, Baltimore
:: DESCRIPTION
LAPD (Linkage Analysis Using Pedigree Data) allows to estimate maximum likelihood allele and two-locus haplotype frequencies, using an Expectation-Maximization algorithm, taking into account family relationships of the individuals.
::DEVELOPER
Computational and Molecular Population Genetics Lab, University of Bern
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Excoffier, L. and Slatkin, M. (1998)
Incorporating genotypes of relatives into a test of linkage disequilibrium,
Am. J. Hum. Genet. 162:171-180.
:: DESCRIPTION
Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. Migrate uses maximum likelihood or Bayesian inference to jointly estimate all parameters.
It can use the following data types:
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Population Genetic Inference With MIGRATE.
Beerli P, Mashayekhi S, Sadeghi M, Khodaei M, Shaw K.
Curr Protoc Bioinformatics. 2019 Dec;68(1):e87. doi: 10.1002/cpbi.87.
:: DESCRIPTION
Genie (Genealogy Interval Explorer) is a program for the inference of demographic history from reconstructed molecular phylogenies. It is primarily designed for the analysis of phylogenies reconstructed from highly variable viral gene sequences, but can be applied to other types of sequence data that contains a significant amount of phylogenetic information.
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Pybus OG, Rambaut. A. 2002.
GENIE: Estimating demographic history from molecular phylogenies.
Bioinformatics 18:1404-5
:: DESCRIPTION
SLIM (Sliding Linear Model) is a software to more reliably estimate π(0) under dependence. When tested on a number of simulation datasets with varying data dependence structures and on microarray data, SLIM was found to be robust in estimating π(0) against dependence. The accuracy of its π(0) estimation suggests that SLIM can be used as a stand-alone tool for prediction of significant tests.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Jan 15;27(2):225-31. Epub 2010 Nov 18.
SLIM: a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures.
Wang HQ, Tuominen LK, Tsai CJ.
:: DESCRIPTION
CLONET is a collection of R scripts which upon estimation of tumor admixture and ploidy infers the clonal hierarchy of genomic aberrations.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Genome Biol. 2014 Aug 26;15(8):439. doi: 10.1186/s13059-014-0439-6.
Unraveling the clonal hierarchy of somatic genomic aberrations.
Prandi D, Baca SC, Romanel A, Barbieri CE, Mosquera JM, Fontugne J, Beltran H, Sboner A, Garraway LA, Rubin MA, Demichelis F.
:: DESCRIPTION
ESPRIT is an algorithm for estimating species richness using large collections of 16S rRNA pyrosequences.
::DEVELOPER
Bioinformatics Laboratory, SUNY Buffalo
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Y. Sun, Y. Cai, L. Liu, F. Yu, M. L. Farrell, W. McKendree, and W. Farmerie,
ESPRIT: Estimating Species Richness Using Large Collections of 16S rRNA Pyrosequences,
Nucleic Acids Research, vol. 37, no. 10, e76, 2009. (impact factor: 7.8)
:: DESCRIPTION
CancerMutationMCMC is a R package for estimating somatic mutation rates and classifying driver and passenger genes in cancer.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
“Hierarchical Bayesian Analysis of Somatic Mutation Data in Cancer“,
Jie Ding, Lorenzo Trippa, Xiaogang Zhong and Giovanni Parmigiani.
Ann. Appl. Stat. Volume 7, Number 2 (2013), 883-903.
