:: DESCRIPTION
ERCS (Extinction/recolonisation coalescent simulator) simulates the coalescent for populations evolving in a spatial continuum under the extinction/recolonisation model.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics (2013) 29 (7): 955-956.
Coalescent simulation in continuous space.
Kelleher J, Barton NH, Etheridge AM.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
msstats Reads in data from Hudson’s coalescent simulation program ms and calculates several common summary statistcs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
sweepsims is the source code from Thornton and Jensen (2007) Controlling the false-positive rate in multilocus genome scans for selection.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
pcrcoal is an R package implementing the coalescent approach to PCR simulation
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Weiss, G, von Haeseler, A (1997)
A coalescent approach to the polymerase chain reaction.
NAR 25(15): 3082-3087
:: 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
:: DOWNLOAD
:: MORE INFORMATION
Citation
Posada D and Wiuf C. 2003.
Simulating haplotype blocks in the human genome.
Bioinformatics 19: 289-290.
