5 evolutionary analyses

5.1 buildTree

5.1.1 Simple template

buildTree(
  scaffold_type = "newick",
  scaffold_in_path = NULL,
  members = NULL
)

5.1.2 Full template

buildTree(
  scaffold_type = c("amin_alignment", "nucl_alignment", "newick"),
  scaffold_in_path = NULL,
  members = NULL,
  gblocks = FALSE, 
  gblocks_path = NULL,
  ml = FALSE, 
  model_test = FALSE,
  bootstrap = FALSE,
  rois = FALSE, 
  rois_data = NULL,
  ancestral_states = FALSE,
  root = NULL
)

5.2 collapseTree