:: DESCRIPTION
SimCopy is an R package simulating the evolution of copy number profiles along a tree. It relies on the PhyloSim package for performing the simulations by encoding the genomic regions as sites in sequences and using modified processes acting on them.
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
indel-Seq-Gen (iSG) is a biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies. This is accomplished through the addition of subsequence length constraints and lineage- and site-specific evolution. iSG tracks insertion and deletion processes that occur during the simulation run. iSG records all evolutionary events and outputs the “true” multiple alignment of the sequences, and can generate a larger simulated sequence space by allowing the use of multiple related root sequences. iSG can be used to test the accuracy of multiple alignment methods, evolutionary hypotheses, ancestral protein reconstruction methods, and protein superfamily classification methods.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Biological sequence simulation for testing complex evolutionary hypotheses: indel-Seq-Gen version 2.0.
Strope CL, Abel K, Scott SD, Moriyama EN.
Mol Biol Evol. 2009 Nov;26(11):2581-93. doi: 10.1093/molbev/msp174.
:: DESCRIPTION
Fatsim is an R-script to simulate the effect of extracting/not extracting lipids on the outcome of stable isotope mixing models
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Tarroux A, Ehrich D, Lecomte N et al. (2010)
Sensitivity of stable isotope mixing models to variation in isotopic ratios: evaluating consequences of lipid extraction.
Methods in Ecology and Evolution, DOI: 10.1111/j.2041-210X.2010.00033.x
:: DESCRIPTION
SPIP (simulate pedigrees in populations) simulates the transmission of genes from parents to offspring in a population having demographic structure defined by the user. Numerous variables controlling the age structure of the population, the number of offspring produced, the variance in male and female reproductive success, survival rates of different age classes, mate fidelity, duration of simulation, etc. can be specified by the user.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Anderson, E. C., and K. K. Dunham.2005.
SPIP 1.0: a program for simulating pedigrees and genetic data in age-structured populations.
Molecular Ecology Notes 5(2):459-461.
:: DESCRIPTION
Simprot is a program to simulate protein evolution by substitution, insertion and deletion
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution
Pang, A., Smith A., Nuin P., and Tillier, E. R. M.,
BMC Bioinformatics (2005) 6: 236
:: DESCRIPTION
Bugsville simulates the genetics of a quantitative character. The user can breed ladybugs to estimate the heritability of spot number, then conduct a selective breeding experiment to see if the heritability multiplied by the selection differential predicts the response to selection.
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:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
AlleleA1 simulates evolution at a single locus in an ideal population of imaginary organisms. The locus of interest has 2 alleles: A1 and A2. The user enters values for parameters controlling selection, mutation, migration, genetic drift, and inbreeding. As the simulation runs, the software plots a graph showing the frequency of allele A1 over time.
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:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Bugs is a simple genetic algorithm program that simulates bacteria-like organisms which move about in a field of “algae” that they eat by moving over them. When they eat enough of the algae, they reproduce by division; if they don’t eat enough, they die. Over time, the initial aimless bugs will evolve into efficient foragers scouring their world for fresh algae.
::DEVELOPER
The Queller/Strassmann Research Group at Washington University in St. Louis
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Sampling is a software for simulating haplotypes in non-equilibrium subdivided populations.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Thomas Städler, Bernhard Haubold, Carlos Merino, Wolfgang Stephan, and Peter Pfaffelhuber
The impact of sampling schemes on the site-frequency spectrum in non-equilibrium subdivided populations
Genetics May 2009 vol. 182 no. 1 205-216
:: DESCRIPTION
yasimSBML ( (Yet another simulator of SBML)) implements a simple method to simulate metabolic network depending on the flux distribution.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
