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