SIMCOAL protocols

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SIMCOAL specifications

Information


Unique identifier OMICS_07256
Name SIMCOAL
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Computer skills Advanced
Version 2.1.2
Stability Stable
Maintained Yes

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Publications for SIMCOAL

SIMCOAL in pipeline

2013
PMCID: 3779339
PMID: 24026825
DOI: 10.1098/rspb.2013.1910

[…] using phylonet5 v. 1.0.0 (a. helgason 2009, unpublished). changes in phylogeographic patterns over time were visualized in gengis []., serial coalescent simulations were run with bayesian serial simcoal [] and analysed in an approximate bayesian computation (abc) framework [] using the abc package in r []. summary statistics (see electronic supplementary material, table s4) were calculated […]


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SIMCOAL in publications

 (32)
PMCID: 5727115
PMID: 29234095
DOI: 10.1038/s41598-017-17728-w

[…] clade credibility was determined using treeannotator and visualized with figtree (http://tree.bio.ed.ac.uk/software/figtree/)., coalescent simulations for 15 y chromosome strs were performed with simcoal v.2.1.2 (http://cmpg.unibe.ch/software/simcoal2/), with the mutation rates used above, a stepwise mutation model with a geometric parameter of 0.1, and a simple population history of two […]

PMCID: 5511155
PMID: 28710389
DOI: 10.1038/s41598-017-05900-1

[…] outlier loci could be adaptive under positive or balancing selection and could exhibit different evolutionary scenarios to neutral loci, , . one million simulations were generated using the package simcoal2 implemented in abctoolbox. the summary statistics were reduced to five partial least-squares components following the instructions in abctoolbox. using the r package abcestimator, […]

PMCID: 5301026
PMID: 28239386
DOI: 10.3389/fpls.2017.00159

[…] traits are derived from the common ancestor or are the consequence of convergence. an approximate bayesian computation (abc) was used to test these evolutionary scenarios. first, package simcoal2 of the abctoolbox was used to generate one million pseudodata for simulation (wegmann et al., ). we used arlsumstat to estimate diversity parameters (e.g., number of alleles, allele […]

PMCID: 4997007
PMID: 27055648
DOI: 10.1093/sysbio/syw028

[…] totalling 30 individual samples. the effective population sizes were set to 1/2*t1 to 8*t1 for all species (t1=1/8ne – 2ne generations). coalescent trees within the species tree were simulated using simcoal () assuming that 1 species represents 1 population and populations merge on speciation events. custom scripts were used to generate input files for simcoal from species trees. twenty-five […]

PMCID: 4785964
PMID: 26998313
DOI: 10.1098/rsos.150250

[…] to compare the different models and identify those that best explain the data, we used an approximate bayesian computation (abc) framework [,] and implemented it together with the bayesian serial simcoal software [,], a program that simulates ancient and modern mtdna data with sample sizes and dates identical to the real data. we also applied two different methods to test for continuity […]


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SIMCOAL institution(s)
Computational and Molecular Population Genetics, Zoological Institute, University of Bern, Bern CH, Switzerland

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