How does TnT (Goloboff et al., 2008) assign internal node labels?

I have used TnT v1.1 (Goloboff et al., 2008) to assign synapomorphies from a presence-absence matrix (PAM) to a phylogeny. TnT does not allow for internal node IDs or branch lengths and I need to use the branch lengths with the TnT data for statistical analyses. I have a huge dataset (>1000 taxa) so assigning branch lengths by hand would be tedious. TnT begins internal node naming based on the first species in the data file (eg if a datafile with 100 species is presented and Aspergillus flavus is the first species, then the node preceding A. flavus is annotated N101). TnT provides internal nodes in its ASCII tree but not in its output newick tree.

Does anyone know how I can either (a) get TnT to print out the internal nodes in a newick tree or how I can replicate TnTs naming procedure, preferably using python (ete2/ete3)?

TIA

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