pcrcoal 1.2.0 – Coalescent Simulations of PCR

pcrcoal 1.2.0

:: DESCRIPTION

pcrcoal is an R package implementing the coalescent approach to PCR simulation

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 pcrcoal

:: MORE INFORMATION

Citation:

Weiss, G, von Haeseler, A (1997)
A coalescent approach to the polymerase chain reaction.
NAR 25(15): 3082-3087

Recodon 1.6.0 / NetRecodon 6.0 – Coalescent Simulation of Intracodon Recombination

Recodon 1.6.0 / NetRecodon 6.0

:: DESCRIPTION

Recodon is able to simulate samples of coding DNA sequences under complex scenarios in which several evolutionary forces can interact simultaneously (namely, recombination, migration and demography). The basic codon model implemented is an extension to the general time-reversible model of nucleotide substitution with a proportion of invariable sites and among-site rate variation. In addition, the program implements non-reversible processes and mixtures of different codon models.

NetRecodon  is a population genetic simulator that generates samples of nucleotide and codon sequences from haploid/diploid populations with intracodon recombination, migration, growth and dated tips. It can also run in several processors using MPI.

::DEVELOPER

Phylogenomics Group at the University of Vigo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

 RecodonNetRecodon

:: MORE INFORMATION

Citation:

Arenas, M. and Posada, D. 2007.
Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography.
BMC Bioinformatics, 8:458.

Arenas M. and Posada, D. 2010.
Coalescent simulation of intracodon recombination.
Genetics, 184(2): 429-437.

msstats 0.3.4 / msff 0.1.6 – Calculates Statistcs of Data from Hudson’s Coalescent Simulation program MS

msstats 0.3.4 / msff 0.1.6

:: DESCRIPTION

msstats Reads in data from Hudson’s coalescent simulation program ms and calculates several common summary statistcs.

msff Applies a frequency filter to the output of Dick Hudson’s coalescent simulation.

::DEVELOPER

Thornton Lab at UC Irvine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 msstats / msff

:: MORE INFORMATION

sweepsims 0.1.2 – Coalescent Simulation Software

sweepsims 0.1.2

:: DESCRIPTION

sweepsims is the source code from Thornton and Jensen (2007) Controlling the false-positive rate in multilocus genome scans for selection.

::DEVELOPER

Thornton Lab at UC Irvine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 sweepsims

:: MORE INFORMATION

Citation

Genetics. 2007 Oct;177(2):987-1000.
The neutral coalescent process for recent gene duplications and copy-number variants.
Thornton KR.

Genetics. 2007 Feb;175(2):737-50.
Controlling the false-positive rate in multilocus genome scans for selection.
Thornton KR, Jensen JD.

PLoS Genet. 2008 Sep 19;4(9):e1000198. doi: 10.1371/journal.pgen.1000198.
An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila.
Jensen JD, Thornton KR, Andolfatto P.

ERCS 1.0.1 – Coalescent Simulations in Continuous Space

ERCS 1.0.1

:: DESCRIPTION

ERCS (Extinction/recolonisation coalescent simulator) simulates the coalescent for populations evolving in a spatial continuum under the extinction/recolonisation model.

::DEVELOPER

Jerome Kelleher

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Python

:: DOWNLOAD

 ERCS

:: MORE INFORMATION

Citation

Bioinformatics (2013) 29 (7): 955-956.
Coalescent simulation in continuous space.
Kelleher J, Barton NH, Etheridge AM.

SNPsim 0.8 – Coalescent Simulation of Hotspot Recombination

SNPsim 0.8

:: DESCRIPTION

SNPsim is a population genetic simulator that generates samples of SNP (Single Nucleotide Polymorphisms) haplotypes and diploid biallelic genotypes.

::DEVELOPER

Phylogenomics Group @ the University of Vigo, Spain

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 SNPsim

:: MORE INFORMATION

Citation

Posada D and Wiuf C. 2003.
Simulating haplotype blocks in the human genome.
Bioinformatics 19: 289-290.