Tag: Bayesian Analysis

BADGER 1.02 beta – Bayesian Analysis of Phylogenies

BADGER 1.02 beta

:: DESCRIPTION

BADGER (Bayesian Analysis to Describe Genomic Evolution by Rearrangement) is a free software package for the Bayesian analysis of phylogenies. The package includes programs for analyzing genome arrangements including mitochondrial DNA The main program uses a variety of Metropolis-Hastings proposal mechanisms to sample from the joint posterior distribution of phylogenetic trees using a model of evolution by reversals of the genomic arrangement. Other programs in the distribution help in analysis of the sampled trees and clades.

::DEVELOPER

Donald Simon & Bret Larget

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • C++ Compiler
  • STL

:: DOWNLOAD

BADGER

:: MORE INFORMATION

CAMBa – Coverage Aware Mutation calling using Bayesian analysis

CAMBa

:: DESCRIPTION

CAMBa is a software of coverage aware mutation calling using bayesian analysis

::DEVELOPER

Vladimir Filkov

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CAMBa

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Jul 14;12:287. doi: 10.1186/1471-2105-12-287.
Statistical mutation calling from sequenced overlapping DNA pools in TILLING experiments.
Missirian V, Comai L, Filkov V.

bamova 1.02 – Bayesian Analysis of Molecular Variance

bamova 1.02

:: DESCRIPTION

bamova implements a Bayesian Analysis of Molecular Variance and different likelihood models for three different types of molecular data (including two models for high throughput sequence data).

::DEVELOPER

Buerkle lab ,University of Wyoming

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 bamova

:: MORE INFORMATION

Citation:

Gompert, Z. and C. A. Buerkle. 2011.
A hierarchical Bayesian model for next-generation population genomics
Genetics March 2011 vol. 187 no. 3 903-917

BADGE 1.0 – Bayesian Analysis of Differential Gene Expression

BADGE 1.0

:: DESCRIPTION

BADGE is a program for the differential analysis of gene expression microarray experiments

::DEVELOPER

Paola Sebastiani

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 BADGE (You will need a password to use this program. Please email sebas@bu.edu for the password.)

:: MORE INFORMATION

Citation

Physiol Genomics. 2005 May 11;21(3):293-8. Epub 2005 Mar 1.
Differential gene expression in pulmonary artery endothelial cells exposed to sickle cell plasma.
Klings ES, Safaya S, Adewoye AH, Odhiambo A, Frampton G, Lenburg M, Gerry N, Sebastiani P, Steinberg MH, Farber HW.

BACOM 1.0 – Bayesian Analysis of COpy number Mixtures

BACOM 1.0

:: DESCRIPTION

BACOM (Bayesian Analysis of COpy number Mixtures) is a statistically-principled in silico approach to accurately estimate genomic deletions and normal tissue contamination, and accordingly recover the true copy number profile in cancer cells. We have developed a cross-platform and open source Java application that implements the whole pipeline of copy number analysis of heterogeneous cancer tissues and other relevant processing steps. We also provide an R interface, bacomR, for running BACOM within the R environment, through which users can smoothly incorporate BACOM into their specific analyses.

::DEVELOPER

Computational Bioinformatics & Bio-imaging Laboratory (CBIL)

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 BACOM

:: MORE INFORMATION

Citation:

BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data.
Yu G, Zhang B, Bova GS, Xu J, Shih IeM, Wang Y.
Bioinformatics. 2011 Jun 1;27(11):1473-80. Epub 2011 Apr 15.

Gmix – Bayesian Analysis of Univariate Normal Mixtures

Gmix

:: DESCRIPTION

Gmix is a program for Bayesian analysis of univariate normal mixtures, in which one component has a fixed mean and possible fixed variance. This model is used in the Biometrics paper “A model-based approach for detecting distinctive gene expression profiles

::DEVELOPER

Dr Alexandra M Lewin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Fortron

:: DOWNLOAD

 Gmix

:: MORE INFORMATION

Citation

Broët, P., Lewin, A., Richardson, S., Dalmasso, C. and Magdelenat, H. (2004)
A mixture model based strategy for selecting sets of genes in multiclass response microarray experiments.
Bioinformatics 2004 20(16):2562-2571;

GenoPlast 1.0 – Bayesian Analysis of Genome Plasticity

GenoPlast 1.0

:: DESCRIPTION

GenoPlast implements a model-based method for using whole genome sequences to infer the patterns of genome content evolution.

::DEVELOPER

Xavier Didelot

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 GenoPlast

:: MORE INFORMATION

Citation

Didelot, Darling and Falush (2009)
Inferring genomic flux in bacteria
Genome Res. 2008., doi:10.1101/gr.082263.108

BAMA – Bayesian Analysis of Multilocus Association

BAMA

:: DESCRIPTION

BAMA is a program to select a trait-associated subset of markers among many candidates. The program is based on Bayesian modeling/estimation and it suits for both quantitative and qualitative traits. It can handle bi- and multiallelic markers as well as applied in situations where part of the marker genotypes may be missing. As an output of the program, one obtains posterior estimate of number and positions of trait-associated markers.

::DEVELOPER

Mikko J. Sillanpää

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

 BAMA

:: MORE INFORMATION

Citation:

R Kilpikari, MJ Sillanpaa (2003),
“Bayesian analysis of multilocus association in quantitative and qualitative traits“,
Genetic Epidemiology, 25:122-135.