Testing different locus lengths to see how length interacts with anomaly zone
Step 1: Set up phylogenetic model
Step 2: Simulate DNA using ipcoal that corresponds to tree (McKenzie and Eaton)
Step 3: Insert missing data between RAD loci and for allele dropout
Step 4: Save true genealogy
Step 5: Run concatenated DNA phlogenetic analysis to confirm in anomaly zone
Step 6: Use ipyrad analysis tool treeslider to estimate phylogeny. Find the optimal window size to capture true relationships.
Step 7: Use Robinson-Foulds distance to calculate distance between trees.
This is a work in progress