percent.identity: Calculate pairwise percent identity.
In BKapili/ppit: Phylogenetic Placement for Inferring Taxonomy

Wrapper function that uses the dist.gene function in ape to calculate pairwise percent identities between query and reference sequences. Loci in input alignment that only contain gaps are removed prior to calculation.

1	percent.identity(type, query, group, alignment_as_matrix)

`type`	Type of query sequence (i.e., "partial" if amplicon or "full" if full-length). For partial sequences, pairwise percent identity calculated based on loci between first and last non-gap amplicon positions in the alignment.
`query`	Name of the query sequence to compare to references.
`group`	Vector of reference sequence names to compare to query sequence.
`alignment`	Nucleotide alignment used for constructing phylogenetic tree of query and reference sequences (e.g., SEPP output alignment).