Conservation genomics of California towhee (Melozone crissalis) in relation to the official list of endangered and threatened wildlife
Andrew N. Black, Jong Yoon Jeon, Chris McCreedy, Safia Janjua, Erangi J Heenkenda, Samarth Mathur, Elise Ferree, Amy L. Fesnock-Parker, Alvaro Hernandez, and J. Andrew DeWoody
Scripts used in each subcategory listed in the manuscript, corresponds to the structure below:
"Reference genome sequencing, assembly, and annotation"
-assembly_safia.sh
"Whole genome resequencing"
-processing/ref_format.sh
-processing/alignment.sh
"Spatial patterns of gene flow"
-analyses/fst-sites.sh
-analyses/fst-sitesF.sh
-analyses/fst-sitesM.sh
-analyses/omni_config.ini
-analyses/towhee_omni.jl
-analyses/towhee_omni.sh
-analyses/towhee_rga.sh
"Genomic diversity"
-analyses/het.sh
-analyses/ROH.sh
"Population structure and differentiation"
-processing/beagle.sh
-analyses/pca.sh
-analyses/admixture.sh
-analyses/clumpp.sh
-analyses/fst.sh
-processing/cleaning_safia.sh
-analyses/bcfcall.sh
-analyses/nu_tree.sh
-analyses/mt_tree.sh
"plotting / summary statistics"
-R/*.R