Creates phylogenetic trees, infers ancestral sequences, and converts the resulting trees into igraph objects. — AntibodyForests_infer

Phylogenetic trees and ancestral sequence reconstruction is performed using the IQ-TREE software. The IQ-TREE directory is required beforehand.

AntibodyForests_infer_ancestral(
  trees,
  alignment.method,
  iqtree.directory,
  collapse.trees,
  parallel
)

Arguments

trees: AntibodyForests object/list of AntibodyForests objects - the resulting sequence similarity or minimum spanning tree networks from the AntibodyForests function.
alignment.method: string - method/software to perform multiple sequence alignment before the ancestral sequence reconstruction step. Options include: 'mafft' (requires the MAFFT software to be locally installed beforehand), 'clustal', 'clustalomega', 'tcoffee', 'muscle', which all require the 'ape' R package.
iqtree.directory: string - path to the IQ-TREE software directory.
collapse.trees: boolean - if T, will collapse the resulting phylogenetic trees if an intermediate daughter sequence/node is the same as its parent.
parallel: boolean - whether to execute the main subroutine in parallel or not. Requires the 'parallel' R package to be installed.

Value

nested list of AntibodyForests objects or single AntibodyForests object, with a modified tree slot including the phylogenetic tree converted into igraph objects and the reconstructed intermediate/ancestral sequences.

Examples

if (FALSE) {
AntibodyForests_infer_ancestral(trees, alignment.method = 'mafft',
igtree.directoty = '/Users/.../Desktop/iqtree-1.6.12-MacOSX')
}