glossary

We try to keep things as simple as possible, but by necessity have developed a bit of lingo. Here are the definitions for some words that you will see in the manual.

placement

An assignment of a single query sequence to a single location in the reference tree. (Contrast with pquery).

pquery

A “placed query” sequence, with uncertainty. In practice this means a collection of placements and their corresponding confidence values (e.g. likelihood weight ratio, etc).

placerun

A collection of pqueries. Short for a run of a placement program.

query sequence

The sequence getting placed into the reference tree. Typically a short read.

reference tree

The fixed tree on which placement occurs.