Tag: Bayesian

bam2mpg 1.0.1 – Bayesian Genotype Caller for NextGen Sequencing Data

bam2mpg 1.0.1

:: DESCRIPTION

bam2mpg calls genotypes from sequence reads of haploid or diploid DNA aligned to a closely-related reference sequence. The program reads alignments in BAM format (http://samtools.sourceforge.net). The MPG (Most Probable Genotype) algorithm is based on a Bayesian model which simulates sampling from one or two alleles with sequencing error, and then calculates the likelihood of each possible genotype given the observed sequence data. Using prior probabilities dependent on the expected heterozygosity of the sequence, MPG then predicts the “Most Probable Genotype” at each site, along with quality scores estimating the accuracy of the calls.

::DEVELOPER

bam2mpg Team  @ NHGRI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 bam2mpg

:: MORE INFORMATION

BAM_ABS – Bayesian Assignment Method for Ambiguous Bisulfite Short Reads

BAM-ABS

:: DESCRIPTION

BAM_ABS is a tool which simulates a Bayesian model that computes the posterior probability of mapping a multiread to each candidate genomic location, taking advantage of uniquely aligned reads.

::DEVELOPER

Professor Zhang Liqing’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

BAM_ABS

:: MORE INFORMATION

Citation

Tran H, Wu X, Tithi S, Sun MA, Xie H, Zhang L.
A Bayesian Assignment Method for Ambiguous Bisulfite Short Reads.
PLoS One. 2016 Mar 24;11(3):e0151826. doi: 10.1371/journal.pone.0151826. PMID: 27011215; PMCID: PMC4806927.

Scythe 0.994 – A Bayesian Adapter Trimmer

Scythe 0.994

:: DESCRIPTION

Scythe is a contaminant/adapter removal tool. It uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in picking out 3′-end adapters, which often include poor quality bases.

::DEVELOPER

UC Davis Bioinformatics Core

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Scythe

:: MORE INFORMATION

JPrIME 0.3.7 – Bayesian Phylogenetics Library in Java

JPrIME 0.3.7

:: DESCRIPTION

JPrIME is a Java library with tools for phylogenetics. It is a complement to the the original C++ library PrIME

::DEVELOPER

JPrIME team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX /Windows
  • Java

:: DOWNLOAD

 JPrIME

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2994-5. doi: 10.1093/bioinformatics/bts548.
DLRS: gene tree evolution in light of a species tree.
Sjöstrand J, Sennblad B, Arvestad L, Lagergren J.

SlidingBayes 0.94 – Exploring Recombination using a Sliding window approach based on Bayesian Phylogenetic inference

SlidingBayes 0.94

:: DESCRIPTION

SlidingBayes is a tool for Bayesian scanning analysis to detect recombination or discordant phylogenetic relationships throughout a nucleotide or amino acid alignment. Bayesian scanning resembles the bootscanning analysis in the way that Bayesian inference analysis is performed in a sliding window of a specified length, and the support of every single clade (approximate posterior probabilities instead of the bootstrap values) is plotted throughout the alignment.

::DEVELOPER

Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research

:: SCREENSHOTS

SlidingBayes

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Java

:: DOWNLOAD

 SlidingBayes

:: MORE INFORMATION

Citation

Bioinformatics. 2005 Apr 1;21(7):1274-5. Epub 2004 Nov 16.
SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference.
Paraskevis D1, Deforche K, Lemey P, Magiorkinis G, Hatzakis A, Vandamme AM.

ScreenBEAM 1.0 – Functional Genomics Screens via Bayesian Hierarchical Modeling

ScreenBEAM 1.0

:: DESCRIPTION

ScreenBEAM is an R package to do gene-level meta-anlaysis of high-throughput functional genomics RNAi or CRISPR screening data. Both microarray and NGS data are supported

::DEVELOPER

Jiyang Yu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 ScreenBEAM

:: MORE INFORMATION

Citation

ScreenBEAM: a Novel Meta-Analysis Algorithm for Functional Genomics Screens via Bayesian Hierarchical Modeling.
Yu J, Silva J, Califano A.
Bioinformatics. 2015 Sep 28. pii: btv556.

BaMFA – Bayesian Metabolic Flux Analysis

BaMFA

:: DESCRIPTION

BaMFA is a matlab package of Bayesian metabolic flux analysis that models the reactions of the whole genome-scale cellular system in probabilistic terms, and can infer the full flux vector distribution of genome-scale metabolic systems based on exchange and intracellular (e.g. 13C) flux measurements, steady-state assumptions, and objective function assumptions.

::DEVELOPER

Computational systems biology group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab

:: DOWNLOAD

BaMFA

:: MORE INFORMATION

Citation

Bioinformatics, 35 (14), i548-i557 2019 Jul 15
Bayesian Metabolic Flux Analysis Reveals Intracellular Flux Couplings
Markus Heinonen et al.

BEGFE 1.1 – Bayesian Estimation of Gene Family Evolution

BEGFE 1.1

:: DESCRIPTION

BEGFE implements a Markov Chain Monte Carlo algorithm to estimate the posterior probability distribution of the birth and death rate parameters and the numbers of gene copies at the internodes of the phylogenetic tree. In addition, BEGFE can simulate gene family data under the birth and death model.

::DEVELOPER

Phylogenetics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/ Windows

:: DOWNLOAD

BEGFE

:: MORE INFORMATION

Citation

Liu, L., L. Yu, V. Kalavacharla, Z. Liu.
A Bayesian model for gene family evolution.
BMC Bioinformatics. 2011, 12:426

BHC 1.1.0 – Bayesian Hierarchical Clustering for R

BHC 1.1.0

:: DESCRIPTION

BHC is an R/Bioconductor port of the fast novel algorithm for Bayesian agglomerative hierarchical clustering.

::DEVELOPER

Warwick Systems Biology Centre

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux/ MacOsX
  • R package

:: DOWNLOAD

 BHC

:: MORE INFORMATION

Citation

BMC Bioinformatics 2009, 10:242
R/BHC: fast Bayesian hierarchical clustering for microarray data
Richard S Savage et al.

BNW – Bayesian Network Web Server

BNW

:: DESCRIPTION

BNW is a comprehensive web server for Bayesian network modeling of biological data sets. It is designed so that users can quickly and seamlessly upload a dataset, learn the structure of the network model that best explains the data, and use the model to understand and make predictions about relationships between the variables in the model.

::DEVELOPER

Yan Cui’s Lab at University of Tennessee Health Science Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BNW

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Nov 1;29(21):2801-3. doi: 10.1093/bioinformatics/btt472. Epub 2013 Aug 21.
Bayesian Network Webserver: a comprehensive tool for biological network modeling.
Ziebarth JD1, Bhattacharya A, Cui Y.

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