Data from: Determining epistatic selection in admixed populations

Schumer M, Brandvain Y

Date Published: April 12, 2016

DOI: http://dx.doi.org/10.5061/dryad.pk20h

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title configuration files and admix'em input file for neutral simulations
Downloaded 1 time
Description Required files to run neutral simulations including three admix'em configuration files for neutral hybrid swarm (admixsimul.cfg), neutral bottleneck hybrid swarm (admixsimul_bottle.cfg), and neutral hybrid swarm with migration simulations (admixsimul_mig.cfg) and other input files to admix'em called by these configuration files
Download neutral_simulations.tar (83.96 Kb)
Details View File Details
Title configuration files and admix'em input file for selection simulations
Downloaded 3 times
Description admix'em configuration files for simulations with epistatic selection under a hybrid swarm (admixsimul.cfg), bottleneck (admixsimul_bottle.cfg) and continuing migration model (admixsimul_mig.cfg) as well as admix'em input files called by these configuration files
Download selection_simulations.tar (75.77 Kb)
Details View File Details
Title simulation shell script
Downloaded 4 times
Description shell script to run admix'em simulations for a given configuration file, number of generations, and number of individuals. NOTE: assumes admixem is installed in the same directory and that the executable is called admixemp. Also assumes that perl and sh scripts provided with this submission are available in the same directory. Usage: perl simulated_ld_shell.pl cfg_file out_folder_name num_iterations focal_gen num_indiv_sample
Download simulated_ld_shell_YB_MS.pl (1.969 Kb)
Details View File Details
Title generate_msg_data_header_200locisim.pl
Downloaded 2 times
Description script to convert admix'em output for the simulation parameters provided to genotype format. This script is called by the simulation shell script: simulated_ld_shell_YB_MS.pl
Download generate_msg_data_header_200locisim.pl (1.65 Kb)
Details View File Details
Title hybrid_index.pl
Downloaded 2 times
Description script to calculate hybrid index from the genotype-format admix'em output for the 200 loci simulated. This script is called by the simulation shell script: simulated_ld_shell_YB_MS.pl
Download hybrid_index.pl (926 bytes)
Details View File Details
Title random_sample.sh
Downloaded 2 times
Description script to subsample the simulated individuals from the genotypes file to the desired number of individuals. This script is called by the simulation shell script: simulated_ld_shell_YB_MS.pl
Download random_sample.sh (146 bytes)
Details View File Details
Title compressed neutral simulation files for reproduction of results figure 2
Downloaded 3 times
Description "neutral.zip" contains neutral simulation results files and scripts needed to reproduce figure 2 in the main text
Download neutral.zip (7.479 Gb)
Details View File Details
Title compressed selection simulation files for reproduction of results figure 3
Downloaded 3 times
Description "selection.zip" contains neutral simulation results files and scripts needed to reproduce figure 3 in the main text
Download selection.zip (10.60 Gb)
Details View File Details

When using this data, please cite the original publication:

Schumer M, Brandvain Y (2016) Determining epistatic selection in admixed populations. Molecular Ecology, online in advance of print. http://dx.doi.org/10.1111/mec.13641

Additionally, please cite the Dryad data package:

Schumer M, Brandvain Y (2016) Data from: Determining epistatic selection in admixed populations. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.pk20h
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: