NewOutgroup filter takes an input tree and (re)root it according to a given species name.
maf.filter= \ [...], NewOutgroup( \ tree_input=BioNJ, \ tree_output=NioNJ_rooted, \ outgroup=outgroupSpecies), \ [...]
The tag name of the tree to reroot.
The tag name to use to store the rerooted tree. If the same as
tree_input, the rerooted tree will replace the old one.
The name of the species to use as outgroup. One and only one sequence for this species should be present in each block for which rerooting is to be performed.
A rooted tree.