Data from: Impact of model violations on the inference of species boundaries under the multispecies coalescent.

Barley AJ, Brown JM, Thomson RC

Date Published: September 1, 2017

DOI: https://doi.org/10.5061/dryad.h6s2k

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Title Simulation in CoMuS for BPP
Downloaded 6 times
Description This python script can be used to simulate datasets under the multispecies coalescent using CoMuS and to setup input files for analyzing these datasets in BPP. Use instructions are contained in the header of the file.
Download Comus_BPP.py (4.058 Kb)
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Title Simulation in CoMuS for STACEY
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Description This python script can be used to simulate datasets under the multispecies coalescent using CoMuS and to setup input files for analyzing these datasets in STACEY. Use instructions are contained in the header of the file.
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Title Simulation in ms for BPP
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Description This python script can be used to simulate coalescent genealogies using ms and sequence datasets using ms, and then to setup input files for analyzing these datasets in BPP. Use instructions are contained in the header of the file.
Download msSimulations_BPP.py (3.949 Kb)
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Title Simulation in ms for STACEY
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Description This python script can be used to simulate coalescent genealogies using ms and sequence datasets using ms, and then to setup input files for analyzing these datasets in STACEY. Use instructions are contained in the header of the file.
Download msSimulations_stacey.py (2.838 Kb)
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Title Posterior prediction in BPP
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Description This python script can be used to perform posterior prediction by sampling the posterior of a BPP analysis, simulating new datasets using McCoal, and setting up input files for analyzing the simulated datasets in BPP. Use instructions are contained in the header of the file.
Download posteriorprediction_BPP.py (8.148 Kb)
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Title Posterior predictive test statistics
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Description This python script can be used to calculate several posterior predictive test statistics using the output from a BPP empirical analysis and the associated posterior predictive BPP analyses. Use instructions are contained in the header of the file.
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Title IbdSim Settings
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Description This text file contains the simulation parameters used for the data simulations done in IBDSim.
Download IbdSettings_file.txt (1.737 Kb)
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Title Supplementary Table 1
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Description This table shows summaries of the dataset characteristics for eight empirical datasets analyzed using posterior prediction.
Download TableS1.pdf (24.31 Kb)
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Title Supplementary Table 2
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Description This table shows summaries of the numbers of species, divergence time, and population size estimates for the empirical data (posterior) and across all posterior predictive datasets (PPD) for the seven datasets analyzed in BPP.
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When using this data, please cite the original publication:

Barley AJ, Brown JM, Thomson RC (2017) Impact of model violations on the inference of species boundaries under the multispecies coalescent. Systematic Biology, online in advance of print. https://doi.org/10.1093/sysbio/syx073

Additionally, please cite the Dryad data package:

Barley AJ, Brown JM, Thomson RC (2017) Data from: Impact of model violations on the inference of species boundaries under the multispecies coalescent. Dryad Digital Repository. https://doi.org/10.5061/dryad.h6s2k
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