Data from: Posterior predictive checks of coalescent models: P2C2M, an R package

Gruenstaeudl M, Reid NM, Wheeler GL, Carstens BC

Date Published: May 28, 2015

DOI: http://dx.doi.org/10.5061/dryad.n715n

 

Files in this package

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Title Figure 2a - Results of sim. 1 - subst. rate s1
Downloaded 18 times
Description Complete file set of data set 1 that was simulated under the multispecies coalescent model and under substitution rate s1. The uncompressed folder constitutes the input for the R package P2C2M to generate the first column of columnspace s1 of Figure 2a.
Download Fig2a_Rate.s1_Sim.001.tar.gz (16.45 Mb)
Download README.txt (1.86 Kb)
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Title Figure 2a - Results of sim. 1 - subst. rate s2
Downloaded 10 times
Description Complete file set of data set 1 that was simulated under the multispecies coalescent model and under substitution rate s2. The uncompressed folder constitutes the input for the R package P2C2M to generate the first column of columnspace s2 of Figure 2a.
Download Fig2a_Rate.s2_Sim.001.tar.gz (16.50 Mb)
Download README.txt (1.839 Kb)
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Title Figure 2b - Results of sim. 1 - subst. rate s1
Downloaded 19 times
Description Complete file set of data set 1 that was simulated in the presence of migration between species and under substitution rate s1. The uncompressed folder constitutes the input for the R package P2C2M to generate the first column of columnspace s1 of Figure 2b.
Download Fig2b_Rate.s1_Sim.001.tar.gz (16.22 Mb)
Download README.txt (1.844 Kb)
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Title Figure 2b - Results of sim. 1 - subst. rate s2
Downloaded 10 times
Description Complete file set of data set 1 that was simulated in the presence of migration between species and under substitution rate s2. The uncompressed folder constitutes the input for the R package P2C2M to generate the first column of columnspace s2 of Figure 2b.
Download Fig2b_Rate.s2_Sim.001.tar.gz (16.27 Mb)
Download README.txt (1.865 Kb)
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Title Simulated Data behind Figure 2a - subst. rate s1
Downloaded 12 times
Description Complete set of nucleotide sequence data alignments simulated on genealogies that were themselves simulated under the multispecies coalescent model and substitution rate s1. The individual files constitute the input for the Python script BEAUTiAutomator.py to generate the XML-formatted input files for *BEAST.
Download SimulatedData_Fig2a_Rate.s1.tar.gz (185.0 Kb)
Download README.txt (1.512 Kb)
Details View File Details
Title Simulated Data behind Figure 2a - subst. rate s2
Downloaded 15 times
Description Complete set of nucleotide sequence data alignments simulated on genealogies that were themselves simulated under the multispecies coalescent model and substitution rate s2. The individual files constitute the input for the Python script BEAUTiAutomator.py to generate the XML-formatted input files for *BEAST.
Download SimulatedData_Fig2a_Rate.s2.tar.gz (147.3 Kb)
Download README.txt (1.511 Kb)
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Title Simulated Data behind Figure 2b - subst. rate s1
Downloaded 14 times
Description Complete set of nucleotide sequence data alignments simulated on genealogies that were themselves simulated in the presence of migration between species and under substitution rate s1. The individual files constitute the input for the Python script BEAUTiAutomator.py to generate the XML-formatted input files for *BEAST.
Download SimulatedData_Fig2b_Rate.s1.tar.gz (180.4 Kb)
Download README.txt (1.517 Kb)
Details View File Details
Title Simulated Data behind Figure 2b - subst. rate s2
Downloaded 12 times
Description Complete set of nucleotide sequence data alignments simulated on genealogies that were themselves simulated in the presence of migration between species and under substitution rate s2. The individual files constitute the input for the Python script BEAUTiAutomator.py to generate the XML-formatted input files for *BEAST.
Download SimulatedData_Fig2b_Rate.s2.tar.gz (144.5 Kb)
Download README.txt (1.517 Kb)
Details View File Details
Title Figure 3 - Loci 5 - Results of sim. 1
Downloaded 16 times
Description Complete file set of data set 1 that comprises a total of five genes. The uncompressed folder constitutes the input for the R package P2C2M to generate the first column of columnspace 'N of loci: 5' of Figure 3.
Download Fig3_Loci.5_Sim.01.tar.gz (10.64 Mb)
Download README.txt (1.863 Kb)
Details View File Details
Title Figure 3 - Loci 10 - Results of sim. 1
Downloaded 14 times
Description Complete file set of data set 1 that comprises a total of ten genes. The uncompressed folder constitutes the input for the R package P2C2M to generate the first column of columnspace 'N of loci: 10' of Figure 3.
Download Fig3_Loci.10_Sim.01.tar.gz (20.76 Mb)
Download README.txt (1.864 Kb)
Details View File Details
Title Figure 3 - Loci 15 - Results of sim. 1
Downloaded 10 times
Description Complete file set of data set 1 that comprises a total of 15 genes. The uncompressed folder constitutes the input for the R package P2C2M to generate the first column of columnspace 'N of loci: 15' of Figure 3.
Download Fig3_Loci.15_Sim.01.tar.gz (30.89 Mb)
Download README.txt (1.861 Kb)
Details View File Details
Title Figure 3 - Loci 20 - Results of sim. 1
Downloaded 15 times
Description Complete file set of data set 1 that comprises a total of 20 genes. The uncompressed folder constitutes the input for the R package P2C2M to generate the first column of columnspace 'N of loci: 20' of Figure 3.
Download Fig3_Loci.20_Sim.01.tar.gz (40.76 Mb)
Download README.txt (1.861 Kb)
Details View File Details
Title Simulated Data behind Figure 3 - Loci 5
Downloaded 11 times
Description Complete set of nucleotide sequence data alignments simulated on genealogies that were themselves simulated under the multispecies coalescent model using a total of five separate genes. The individual files constitute the input for the Python script BEAUTiAutomator.py to generate the XML-formatted input files for *BEAST. This set of data was used to generate columnspace 'N of loci: 5' of Figure 3.
Download SimulatedData_Fig3_Loci.5.tar.gz (504.8 Kb)
Download README.txt (1.506 Kb)
Details View File Details
Title Simulated Data behind Figure 3 - Loci 10
Downloaded 16 times
Description Complete set of nucleotide sequence data alignments simulated on genealogies that were themselves simulated under the multispecies coalescent model using a total of ten separate genes. The individual files constitute the input for the Python script BEAUTiAutomator.py to generate the XML-formatted input files for *BEAST. This set of data was used to generate columnspace 'N of loci: 10' of Figure 3.
Download SimulatedData_Fig3_Loci.10.tar.gz (982.2 Kb)
Download README.txt (1.51 Kb)
Details View File Details
Title Simulated Data behind Figure 3 - Loci 15
Downloaded 11 times
Description Complete set of nucleotide sequence data alignments simulated on genealogies that were themselves simulated under the multispecies coalescent model using a total of 15 separate genes. The individual files constitute the input for the Python script BEAUTiAutomator.py to generate the XML-formatted input files for *BEAST. This set of data was used to generate columnspace 'N of loci: 15' of Figure 3.
Download SimulatedData_Fig3_Loci.15.tar.gz (1.509 Mb)
Download README.txt (1.508 Kb)
Details View File Details
Title Simulated Data behind Figure 3 - Loci 20
Downloaded 11 times
Description Complete set of nucleotide sequence data alignments simulated on genealogies that were themselves simulated under the multispecies coalescent model using a total of 20 separate genes. The individual files constitute the input for the Python script BEAUTiAutomator.py to generate the XML-formatted input files for *BEAST. This set of data was used to generate columnspace 'N of loci: 20' of Figure 3.
Download SimulatedData_Fig3_Loci.20.tar.gz (1.979 Mb)
Download README.txt (1.508 Kb)
Details View File Details

When using this data, please cite the original publication:

Gruenstaeudl M, Reid NM, Wheeler GL, Carstens BC (2015) Posterior predictive checks of coalescent models: P2C2M, an R package. Molecular Ecology Resources 16(1):193-205. http://dx.doi.org/10.1111/1755-0998.12435

Additionally, please cite the Dryad data package:

Gruenstaeudl M, Reid NM, Wheeler GL, Carstens BC (2015) Data from: Posterior predictive checks of coalescent models: P2C2M, an R package. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.n715n
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