PyRate 2.0 – Bayesian Estimation of Speciation and Extinction from Fossil Data

PyRate 2.0

:: DESCRIPTION

PyRate is a Python program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework.

::DEVELOPER

The Computational Phylogenetics group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python

:: DOWNLOAD

 PyRate

:: MORE INFORMATION

Citation

Silvestro, D., J. Schnitzler, L. H. Liow, A. Antonelli, and N. Salamin. 2014.
Bayesian estimation of speciation and extinction from incomplete fossil occurrence data.
Systematic Biology doi:10.1093/sysbio/syu006.

Cyber-TPlus – Analysis of Differential Gene Expression Based on Bayesian Estimation of Variance

Cyber-TPlus

:: DESCRIPTION

Cyber-TPlus is a differential analysis tool that uses Bayesian estimation of the variance of gene expression level for the small number of replicates. The method has more consistent comparing to the widely used tool cyber-t that successfully introduced Bayesian framework into differential analysis.

::DEVELOPER

Systems Biology of Gene Regulatory Elements

:: SCREENSHOTS

Cyber-TPlus

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  •  java

:: DOWNLOAD

 Cyber-TPlus

:: MORE INFORMATION

BASELINe 1.3 – Bayesian Estimation of Antigen-Driven Selection in Immunoglobulin Sequences

BASELINe 1.3

:: DESCRIPTION

BASELINe, a new computational framework for Bayesian estimation of Antigen-driven selection in Immunoglobulin sequences, provides a more intuitive means of analyzing selection by actually quantifying it.

::DEVELOPER

Kleinstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 BASELINe

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Sep 1;40(17):e134. Epub 2012 May 27.
Quantifying selection in high-throughput Immunoglobulin sequencing data sets.
Yaari G1, Uduman M, Kleinstein SH.

PurBayes 1.3 – Bayesian Estimation of Tumor Purity and Clonality

PurBayes 1.3

:: DESCRIPTION

PurBayes is an MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data.

::DEVELOPER

Nicholas B. Larson <larson.nicholas at mayo.edu>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 PurBayes

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 1;29(15):1888-9. doi: 10.1093/bioinformatics/btt293. Epub 2013 Jun 6.
PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data.
Larson NB1, Fridley BL.

bgc 1.03 – Bayesian Estimation of Genomic Clines

bgc 1.03

:: DESCRIPTION

bgc  implements Bayesian estimation of genomic clines to quantify introgression at many loci. Models are available for linked loci, genotype uncertainty and sequence errors. Models for genotype uncertainty and sequence error can be used to estimate genomic cline parameters from next-generation sequence data.

::DEVELOPER

Buerkle lab ,University of Wyoming

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 bgc

:: MORE INFORMATION

Citation:

bgc: Software for Bayesian estimation of genomic clines.
Gompert Z, Buerkle CA.
Molecular Ecology Resources, 2012 Nov;12(6):1168-76. doi: 10.1111/1755-0998.12009.x. Epub 2012 Sep 14.

BEDASSLE 1-1 – Bayesian Estimation of Differentiation in Alleles by Spatial Structure and Local Ecology

BEDASSLE 1-1

:: DESCRIPTION

BEDASSLE estimates the relative contributions of pairwise geographic distance and pairwise ecological distance to patterns of genetic variation.

::DEVELOPER

Gideon Bradburd  with Peter Ralph and Graham Coop

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BEDASSLE

:: MORE INFORMATION

Citation

Evolution. 2013 Nov;67(11):3258-73. doi: 10.1111/evo.12193.
Disentangling the effects of geographic and ecological isolation on genetic differentiation.
Bradburd GS, Ralph PL, Coop GM.

BAYESFST – Bayesian Estimation of Coancestry Coefficient FST

BAYESFST

:: DESCRIPTION

BAYESFST , Bayesian estimation of the coancestry coefficient FST

::DEVELOPER

Department of Mathematics and Statistic , The University of Reading

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BAYESFST

:: MORE INFORMATION

Citation:

Beaumont, Balding (2004),
Identifying adaptive genetic divergence among populations from genome scans“,
Molecular Ecology, 13:969-980.