Tag: – Approximate Bayesian Computation

CodABC 2.0.0b – Coestimation of Recombination, Substitution and Molecular Adaptation Rates by Approximate Bayesian Computation

CodABC 2.0.0b

:: DESCRIPTION

The package CodABC is computer framework to coestimate Recombination, Substitution and Molecular Adaptation (dN/dS) rates by approximate Bayesian computation from coding sequence alignments.

::DEVELOPER

Dr. MIGUEL ARENAS

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

  CodABC

:: MORE INFORMATION

Citation

Mol Biol Evol. 2015 Apr;32(4):1109-12. doi: 10.1093/molbev/msu411. Epub 2015 Jan 9.
CodABC: A Computational Framework to Coestimate Recombination, Substitution, and Molecular Adaptation Rates by Approximate Bayesian Computation.
Arenas M, Lopes JS, Beaumont MA, Posada D

ABCtoolbox – Toolkit to perform Approximate Bayesian Computations

ABCtoolbox

:: DESCRIPTION

ABCtoolbox was designed to perform Approximate Bayesian Computation (ABC) estimations using various recently published algorithms including MCMC without likelihood and Population Monte Carlo. Due to its potential to interact with almost any command line simulation software, ABCtoolbox can be used to study problems in different areas including genomics or population genetics.

::DEVELOPER

Computational and Molecular Population Genetics Lab, University of Bern

:: SCREENSHOTS

n/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 ABCtoolbox

:: MORE INFORMATION

Citation

Wegmann, D, Leuenberger C, Neuenschwander S, Excoffier L (2010)
ABCtoolbox: a versatile toolkit for approximate Bayesian computations.
BMC Bioinformatics 11: 116.

ABCreg 0.1.0 – Automating Approximate Bayesian Computation by Local Linear Regression

ABCreg 0.1.0

:: DESCRIPTION

ABCreg is a tool for performing statistical inference via approximate Bayesian computation, or ABC.

::DEVELOPER

Thornton Lab at UC Irvine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 ABCreg

:: MORE INFORMATION

Citation

BMC Genet. 2009 Jul 7;10:35. doi: 10.1186/1471-2156-10-35.
Automating approximate Bayesian computation by local linear regression.
Thornton KR

DIYABC 2.1.0 – Approximate Bayesian Computation for Inference on Population history

DIYABC 2.1.0

:: DESCRIPTION

DIYABC is a computer program with a graphical user interface and a fully click-able environment. It allows population biologists to make inference based on Approximate Bayesian Computation (ABC), in which scenarios can be customized by the user to fit many complex situations involving any number of populations and samples. Such scenarios involve any combination of population divergences, admixtures and population size changes. DIYABC can be used to compare competing scenarios, estimate parameters for one or more scenarios, and compute bias and precision measures for a given scenario and known values of parameters (the current version applies to unlinked microsatellite data).

::DEVELOPER

The Center for Biology and Management of Populations @ CBGP

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 DIYABC

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jan 13.
DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data.
Cornuet JM1, Pudlo P, Veyssier J, Dehne-Garcia A, Gautier M, Leblois R, Marin JM, Estoup A.

BMC Bioinformatics. 2010 Jul 28;11:401.
Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0).
Cornuet JM, Ravigné V, Estoup A.