buildTree: Construct various types of phylogenetic trees from alignments...

In LucasBusta/phyloChemistry: Chemical and Sequence Analyses in a Phylogenetic Context

Description

Construct various types of phylogenetic trees from alignments or other trees

Usage

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

Arguments

scaffold_type	The type of information that should be used to build the tree. One of "amin_alignment", "nucl_alignment", or "newick"
scaffold_in_path	The path to the information that should be used to build the tree.
members	The tips of the tree that should be included. Default is to include everything.
gblocks	TRUE/FALSE whether to use gblocks on the alignment
gblocks_path	Path to the gblocks module
ml	TRUE/FALSE whether to use maximum likelihood when constructing the tree.
model_test	TRUE/FALSE whether to test various maximum likelihood models while constructing the tree
bootstrap	TRUE/FALSE whether to calculate bootstrap values for tree nodes.
rois	TRUE/FALSE whether to use only certain portions of an alignment for constructing the tree
rois_data	The position in the alignment to use when constructing the tree. Default = NULL, i.e. all positions.
ancestral_states	TRUE/FALSE whether to calculate ancestral states at nodes in the tree. Requires specifying a root via the 'root' parameter
root	The tree tip to use as the root of the tree

LucasBusta/phyloChemistry documentation built on Sept. 6, 2020, 11:36 p.m.