tree.partition: Determine optimal phylogenetic neighborhood threshold.
In BKapili/ppit: Phylogenetic Placement for Inferring Taxonomy

Determines patristic distance threshold that maximizes the number of host inferences returned at the phylum rank.

1	tree.partition(type, query, tree, alignment, taxonomy, cutoffs)

`query`	Vector of query sequence names.
`tree`	Phylogenetic tree in Newick format containing query sequences placed onto a reference tree.
`alignment`	Nucleotide alignment used for constructing phylogenetic tree of query and reference sequences (e.g., SEPP output alignment).
`taxonomy`	Data frame containing taxonomic information and genomic location for each reference sequence.
`cutoffs`	Data frame containing patristic distance and pairwise percent identity cutoffs for each taxonomic rank.