Basic Package AttributesAttribute  Value 

Title  mlcoalsim 

Short Description  Multilocus Coalescent Simulations 

Long Description  The application program mlcoalsim (multilocus coalescent simulations) is designed to: (i) Generate samples and calculate neutrality tests, and other statistics, under stationary model, several demographic models or strong positive selection by mean of coalescent theory. (i) Perform coalescent simulations with the mutational phase given: 1. the population mutation rate θ (θ = 4Nμ, where N is the effective population size and μ is the mutational rate). 2. a fixed number of mutations. 3. a distribution of θ values. A prior uniform (bounded) and a gamma distributions are enabled. 4. a fixed number of biallelic segregating sites taking into account the uncertainty of the population mutation rate (conditioning on biallelic segregating sites). A prior uniform (bounded) and a gamma distributions are enabled. (iii) Perform coalescent simulations with recombination given: 1. the population recombination rate R (R = 4Nr, where r is the recombination rate). 2. a distribution of r values. A prior uniform (bounded) and a gamma distributions are enabled. 3. a fixed number of minimum recombination events (Rm) taking into account the uncer tainty of the population recombination rate (fixing Rm). A prior uniform (bounded) and a gamma distributions are enabled. 4. a fixed number of minimum recombination events (Rm) and a fixed number of haplo types, considering the uncertainty of the population recombination rate. (iv) Perform multilocus analyses. Linked loci and unlinked loci are enabled. Multilocus statistics for unlinked loci are the average and the variance for each statistic. (v) Include recurrent mutations (multiple hits) or not. (vi) Include heterogeneity in mutation rate across the length of the sequence. A gamma distri bution is used. Also, a number of invariant positions can also be defined. (vii) Include heterogeneity in recombination rate across the length of the sequence. A gamma distribution is used. Hotspots or a constant value for all positions are possible. This program is based on a previous version of Hudson’s coalescent program ms (Hudson, 2002) and modified for the above purposes. The function to calculate minimum recombinant values is a modification of Wall’s code (Wall, 2000). The gamma function was partially obtained from Grassly, Adachi and Rambaut code (Grassly et al., 1997). This program is distributed under the GNU GPL License.
Version 2 includes parallel computation for multiple locus and the possibility to include priors for each of the parameters (useful for ABC computation analysis). The input file has been modified.


Version  v2 

Project Started  2008 

Last Release  6 years, 11 months ago 

Homepage  http://code.google.com/p/mlcoalsimv1/ 

Citations 
RamosOnsins SE, MitchellOlds T, Mlcoalsim: multilocus coalescent simulations., Evol Bioinform Online, March 2, 2007
[Abstract, cited in
PMC
]


GSR Certification 
This simulator has not yet been evaluated for GSR Certification. Learn more about or request GSR Certification.


Detailed AttributesAttribute Category  Attribute 

Target  

Type of Simulated Data  Haploid DNA Sequence,


Variations  Biallelic Marker,


Simulation Method  Standard Coalescent,


Input  

Data Type  

File format  

Output  

Data Type  Genotype or Sequence,
Diversity Measures,


Sequencing Reads  Other,


File Format  MS,


Sample Type  

Phenotype  

Trait Type  

Determinants  

Evolutionary Features  

Demographic  

Population Size Changes  Constant Size,
Carrying Capacity,


Gene Flow  Island Models,
Userdefined Matrix,


Spatiality  

Life Cycle  

Mating System  Random Mating,


Fecundity  

Natural Selection  

Determinant  

Models  Directional Selection,


Recombination  Varying Recombination Rates,


Mutation Models  Heterogeneity among Sites,


Events Allowed  

Other  

Interface  Commandline,
Graphical User Interface,
Scriptbased,


Development  

Tested Platforms  Windows,
Mac OS X,
Linux and Unix,


Language  C or C++,


License  GNU Public License,


GSR Certification  

No example publication using mlcoalsim has been provided.
Please
propose new citations if you are aware of publications that use this software.