:: DESCRIPTION
MixSIH is a probabilistic model for solving the single individual haplotyping (SIH) or haplotype assembly problem.
::DEVELOPER
hirotaka MATSUMOTO , Kiryu Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Genomics. 2013;14 Suppl 2:S5. doi: 10.1186/1471-2164-14-S2-S5.
MixSIH: a mixture model for single individual haplotyping.
Matsumoto H, Kiryu H.
:: DESCRIPTION
Mixer is a mixture model approach to analyze ChIP-chip or ChIP-seq data, also with some utility functions to process DNA sequence data. It includes statistical methods for both data normalization and peak detection. The peak detection and quantification relies on a mixer model approach that dissects the distribution of background signals and the Immunoprecipitated signals. In contrast to many existing methods, mixer is more flexible by imposing less restrictive assumptions and allowing a relatively large proportion of peak regions. Robust performance on data sets predicted to contain numerous peaks is very important for the studies of the transcription factors with abundant binding sites, and common chromatin features or epigenetic marks.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wei Sun, Michael J Buck, Mukund Patel and Ian J Davis (2009),
Improved ChIP-chip analysis by mixture model approach.
BMC Bioinformatics 2009, 10:173
:: DESCRIPTION
PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. Compared to other phylogenetic MCMC samplers (e.g. MrBayes), the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT. It is particularly well suited for large multigene alignments, such as those used in phylogenomics.
::DEVELOPER
Nicolas Lartillot (nicolas.lartillot@umontreal.ca)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nicolas Lartillot, Thomas Lepage and Samuel Blanquart
PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
Bioinformatics (2009) 25 (17): 2286-2288.
:: DESCRIPTION
MixNet (Erdös-Renyi Mixture for Networks) is the first publicly available computer software that analyzes biological networks using mixture models.This model is based on the hypothesis that real networks are made of classes which show specific connectivity patterns.
The MixeR allows the use of the basical options of MixNet software and the post-treatment of the results.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Picard, F., Miele, V., Daudin,J-J., Cottret,L., Robin, S.,
Deciphering the connectivity structure of biological networks using MixNet,
MC Bioinformatics. 2009 Jun 16;10 Suppl 6:S17. doi: 10.1186/1471-2105-10-S6-S17.
:: DESCRIPTION
HTTMM is a package designed for estimating the abundance of taxon within a microbial community by incorporating the structure of the taxonomy tree.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
IEEE/ACM Trans Comput Biol Bioinform. 2015 Sep-Oct;12(5):1112-22. doi: 10.1109/TCBB.2015.2415814.
Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree.
Qiu YQ, Tian X, Zhang S.
:: DESCRIPTION
MixClone is a comprehensive software package to study the subclonal structures of tumor genomes, including subclonal cellular prevalences estimation, allelic configuration estimation, absolute copy number estimation and a few visualization tools
::DEVELOPER
CBCL Lab (Computational Biology and Computational Learning) @ UCI
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Genomics. 2015;16 Suppl 2:S1. doi: 10.1186/1471-2164-16-S2-S1. Epub 2015 Jan 21.
MixClone: a mixture model for inferring tumor subclonal populations.
Li Y, Xie X.
:: DESCRIPTION
VarMixt is an efficient variance modelling for the differential analysis of replicated gene expression data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2005 Feb 15;21(4):502-8.
VarMixt: efficient variance modelling for the differential analysis of replicated gene expression data.
Delmar P, Robin S, Daudin JJ.
:: DESCRIPTION
DIME (Differential Identification using Mixtures Ensemble) is an ensemble of methods for differential analysis. Specifically, it considers an ensemble of finite mixture models combined with a local false discovery rate (fdr) for analyzing ChIP-seq data comparing two samples. This package can also be used to identify differential in other high throughput data such as microarray and DNA methylation.
::DEVELOPER
Statistical Genetics and Bioinformatics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Taslim, C., Huang, T., and Lin, S. (2011).
DIME: R-package for Identifying Differential ChIP-seq Based on an Ensemble of Mixture Models.
Bioinformatics, 27, 1569-1570.
:: DESCRIPTION
fitGCP is a framework for fitting mixtures of probability distributions to genome coverage profiles. Besides commonly used distributions, fitGCP uses distributions tailored to account for common artifacts. The mixture models are iteratively fitted based on the Expectation-Maximization algorithm.
::DEVELOPER
JRG 4: Bioinformatics Research Group Bioinformatics (NG4), Robert Koch-Institut
: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Analyzing genome coverage profiles with applications to quality control in metagenomics
Martin S. Lindner, Maximilian Kollock, Franziska Zickmann and Bernhard Y. Renard,
Bioinformatics (2013) 29 (10): 1260-1267.
:: DESCRIPTION
Mtreemix is a software package to estimate mixture models of mutagenetic trees from observed cross-sectional data. Mutagenetic tree mixtures are probabilistic models that have been designed to describe evolutionary processes that are characterized by the accumulation of genetic changes. Mtreemix has been applied to model the development of drug resistance-associated mutations in the HIV genome and the accumulation of chromosomal gains and losses in tumor development.
::DEVELOPER
Dr. Niko Beerenwinkel , Max-Planck-Institut Informatik
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Beerenwinkel, N.; Rahnenführer, J.; Kaiser, R.; Hoffmann, D.; Selbig, J.; Lengauer, T.,
Mtreemix: a software package for learning and using mixture models of mutagenetic trees.
Bioinformatics 2005, 21 (9), 2106-7.
