Elimia-Population-Genomics

Scripts and command line from study on spring-obligate pleurocerid snails in Alabama.

Raw data and files can be found at (https://figshare.com/articles/dataset/Unique_Genetic_Diversity_Patterns_and_Extreme_Endemism_in_Temperate_Springs_Evidence_from_Narrow-Range_Endemic_Snails/25884100)

Scripts and Command Line used During Data Analysis

The following are sample scripts used for a single dataset:

• AMOVA_Elimia_bellacrenata.R
• Admixture_LEA.R
• Fstat_Calculation.R
• OrientAGraph_Visualization.R
• SNAQ_Visualization.R
• SNAQ_Command_Line.txt

The following are samples of scripts that were used with several datasets:

• BayesScan_R_Visualization.R
• Fastsimcoal2_CommandLine.txt
• Fastsimcoal2_Demographic_Analyses.R
• RADpainter_Standard_Visualization.R

Check These Repositories for the Most Current Version of the Following Scripts

Convert_Stacks_Fasta_to_Loci.py - https://github.com/dportik/Stacks_pipeline/tree/master/stacks-pipeline-scripts

FASconCAT-G_v1.05.1.pl - https://github.com/PatrickKueck/FASconCAT-G

vcf2dadi.py - https://github.com/CoBiG2/RAD_Tools/blob/master/vcf2dadi.py

2b-RAD Processing Scripts - https://github.com/NathanWhelan/2bRAD-processing