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.. _glossary:

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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.