btmartin721/ClineHelpR: Parses and Plots BGC and INTROGRESS Output

Aggregates multiple BGC runs, plots LnL traces, and associates GFF annotations with genomic scaffolds that were also run through BGC. Then, it makes the Hybrid Index X Phi plots from Gompert et al. (2012), and plots trascriptome and scaffold loci onto ideograms. The INTROGRESS functions run INTROGRESS genomic clines then associate environmental raster layers with the INTROGRESS genomic clines. MAXENT is run on a folder of raster layers (e.g., the 19 BIOCLIM layers) and sample localities to determine the most important layers, and genomic cline X environment plots are generated using the most important layers.

install.packages("remotes")
remotes::install_github("btmartin721/ClineHelpR")