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GSR: Simulator - Bayesian Serial SimCoal
| Attribute | Value |
|---|---|
| Title | Bayesian Serial SimCoal |
| Short Description | Bayesian Serial SimCoal, (BayeSSC) is a modification of SIMCOAL 1.0, a program written by Laurent Excoffier, John Novembre, and Stefan Schneider. |
| Long Description | Bayes SSC is powerful because it allows flexible coalescent modelling from a variety of different priors. The enables parameter estimation, likelihood calculations, and Bayesian inference. Typically, BayeSSC generates thousands of hypothetical trees using slightly different population parameters. The simulated genetics of these trees can then be compared to the actual genetics of the user's samples to investigate which history of these many simulated histories is the most likely to have generated the samples. |
| Project Started | 2009 |
| Last Release | 13 years ago |
| Homepage | http://www.stanford.edu/group/hadlylab/ssc/index.html |
| Citations | Excoffier L, Novembre J, Schneider S, SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography., J Hered, 11-01-2000 [ Abstract, cited in PMC ] |
| GSR Certification | Accessibility |
| Last evaluated | 02-08-2018 (2256 days ago) |
| Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Haploid DNA Sequence, |
| Variations | Single Nucleotide Variation, |
| Simulation Method | Standard Coalescent, |
| Input | |
| Data Type | Allele Frequencies, |
| File format | Arlequin, NEXUS, |
| Output | |
| Data Type | Genotype or Sequence, Individual Relationship, Diversity Measures, |
| Sequencing Reads | Other, |
| File Format | Arlequin, |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Exponential Growth or Decline, User Defined, |
| Gene Flow | User-defined Matrix, |
| Spatiality | |
| Life Cycle | |
| Mating System | Random Mating, |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | k-Allele Model, Heterogeneity among Sites, |
| Events Allowed | Varying Demographic Features, |
| Other | |
| Interface | Command-line, Script-based (R), |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | C or C++, R, |
| License | GNU Public License, |
| GSR Certification | Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used Bayesian Serial SimCoal.
2020
Zvénigorosky V, Duchesne S, Romanova L, Gérard P, Petit C, Petit M, Alexeev A, Melnichuk O, Gonzalez A, Fausser JL, et al., The genetic legacy of legendary and historical Siberian chieftains., Commun Biol, 10-16-2020 [Abstract]
1993
Iakobson MG, Krivoshapkin AL, Savelov AA, Shterental' ISh, Rabinovich SS, Strel'tsova GP, Strygin AV, Malkova NA, [Magnetic resonance tomography in the diagnosis of tumor processes in the area of the cerebellopontile angle]., Zh Vopr Neirokhir Im N N Burdenko, 07-01-1993 [Abstract]