buildPhylogeneticTree | R Documentation |
Uses FastTree[MP] to generate a maximum likelihood tree based on sequence profiles.
buildPhylogeneticTree(path.2.cds.msa, path.2.ml.tree,
fast.tree.call = getOption("fast.tree.call", paste("OMP_NUM_THREADS=",
getOption("mc.cores", 1), " FastTreeMP -nt -gtr -gamma", sep = "")))
'path.2.cds.msa' |
a valid file path to the codon multiple sequence alignment to feed into FastTree[MP] |
'path.2.ml.tree' |
a valid file path in which to store the resulting tree in newick format |
'fast.tree.call' |
the command whith which to invoke FastTree[MP] |
TRUE if and only if no error occurred.
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