The program gotree could be used to perform a midpoint rooting (Farris 1972) on the unrooted phylogenetic tree contained in the NEWICK-formatted file $intree. The following command line writes the resulting rooted tree into the file $outtree:
The program gotree could be used to root a phylogenetic tree contained in the NEWICK-formatted file $intree by using one of several taxon names specified in the string $outgroup (each separated by blank spaces) and write the resulting tree into the filr $outtreewith the following command line:
Of note, to obtain an unrooted tree (i.e. with the outgroup placed on the top-level trifurcation), the following command line should be used: