View source: R/AntibodyForests_infer_ancestral.R
AntibodyForests_infer_ancestral | R Documentation |
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 )
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. |
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.
## Not run: AntibodyForests_infer_ancestral(trees, alignment.method = 'mafft', igtree.directoty = '/Users/.../Desktop/iqtree-1.6.12-MacOSX') ## End(Not run)
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