The code below may be distributed publicly, provided that it is cited appropriately. I have begun depositing code (mainly in R) to my GitHub repository (https://github.com/MarisaBSzubryt), but more extensive documentation can be found here as well.

Generating county level maps from coordinates or state-county data:
The code below can be used to generate county-level maps for the contiguous United States, either for one taxon (one color) or multiple taxa (multiple colors). Input data can either take the form of coordinates (“decimalLatitude” and “decimalLongitude”), state and county data (“stateProvince” and “county”), or a list of formatted state-county strings.
https://github.com/MarisaBSzubryt/MBS_County_Maps

Extracting and plotting gene tree statistics (bootstrap support values, bipartition values, and internal tree length (root-to-tip variance) values can be accomplished through a combination of Unix (with the help of phyx and SortaDate) and R. To gather more insight about target-capture or HybSeq data, see the GitHub repository below.
https://github.com/MarisaBSzubryt/MBS_Extracting_Gene_Tree_Statistics