A rapid coalescent-based whole genome simulator Long Description (required) GENOME is a program to simulate sequences drawn from a population under the Wright-Fisher neutral model (Ewens 1979). It is based on a standard coalescent model (Hudson 1983, 1990; Donnelly & Tavaré 1995). Starting with the sampled sequences and moving backward in time, coalescent, recombination and migration events are simulated at each generation. These events could occur multiple times and could happen in the same generation. Each coalescent event is recorded and the resulting genealogy tree is constructed. Demographic events such as population bottlenecks and expansions or population merges and splits can also be simulated. In addition to uniform recombination rates, it is possible to allow recombination rates to vary so as to mimic the pattern of hotspots along the genome. After simulating a coalescent tree, mutations are placed along each branch. The number of mutations on each branch follows a Poisson distribution with mean equal to the product of the mutation rate and the branch length. The infinite-site mutation model is assumed, so no recurrent mutation can occur. The genealogy tree can also be output in Newick format, which is identical to that used by programs such as PHYLIP (Felsenstein 2005) and seq-gen (Rambaut & Grassly 1997).
The program is written in C++ and is portable to multiple operating systems. The following sections will describe how to download and compile the program and how
to specify the parameters for the program. http://csg.sph.umich.edu/liang/genome/ Step 1: Use the attribute tree to add new attributes or remove pre-selected attributes to describe the simulator. Every sub-attribute is selected Not all sub-attributes are selected Fill Clear Expand Collapse Reset Summary of Proposed Changes Step 2: Review list of proposed attribute addition(s) and subtraction(s). Can't Find the Attribute You Are Looking For?
If you would like to propose an attribute that you cannot find in the tree above, or if you would like to add a clarification to one or more attributes for this simulator (e.g. a specific file format for attribute /Output/File Format/Other), please list them in the
Additional Comment box of the Submit tab. Summary of Proposed Changes Current Citations/Applications
GENOME: a rapid coalescent-based whole genome simulator. Bioinformatics,
https://www.ncbi.nlm.nih.gov/pubmed/?term=17459963, Primary Citation
The variance of identity-by-descent sharing in the Wright-Fisher model. Genetics,
https://www.ncbi.nlm.nih.gov/pubmed/?term=23267057, , Application
Inference of historical migration rates via haplotype sharing. Bioinformatics,
https://www.ncbi.nlm.nih.gov/pubmed/?term=23812983, , Application