ppit: Infer host identities of query sequences.
In BKapili/ppit: Phylogenetic Placement for Inferring Taxonomy

Function that infers taxonomic identity of marker gene source organisms based on phylogenetic placement and sequence identity. For a tutorial, type Vignette('ppit').

1	ppit(type, query, tree, alignment, taxonomy, opt_thresh, cutoffs)

`type`	Either "partial" or "full".
`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).
`opt_thresh`	Phylogenetic neighborhood threshold.
`cutoffs`	Data frame containing patristic distance and pairwise percent identity cutoffs for each taxonomic rank.