This folder contains scripts and command lines used in an experimental-adaptive-radiation project (Genomic signatures of experimental adaptive radiation in Drosophila). Please note that some of scripts and command lines might be restrictive and can run exclusively on VT ARC cluster (www.arc.vt.edu).

Contents:

[01.mappingAndGenotyping.sh]

Command lines of mapping and genotyping for sample 1A, all other samples can be processed in similar way.

[02.estimates.sh]

R commands for Ne estimates and s (selection coefficient) estimates for CS regime, other regimes can be processed in the same manner.

[03.simulation.sh]

Command lines for neutral simulation using data from the DGRP2 (Drosophila Genetic Reference Panel 2).

[04.sweep.sh]

Command lines of sweep detection for selection regime CS of generation 65, all other samples can be processed in the same way.

[05.TE.sh]

Command lines of (transposoble element) TE identification for selection regime CS of generation 65.

[06.PCA.sh]

Command lines for PCA using eigensoft (https://www.hsph.harvard.edu/alkes-price/software/).

[07.haplotypeBlockReconstruction.sh]

R command lines of haplotype block reconstruction for selection regime CS.