title: Aligning short reads to reference alignments and trees.
abstract: BACKGROUND
  Likelihood-based methods for placing short read sequences from metagenomic samples into reference phylogenies have been recently introduced. At present, it is unclear how to align those reads with respect to the reference alignment that was deployed to infer the reference phylogeny. Moreover, the adaptability of such alignment methods with respect to the underlying reference alignment strategies/philosophies has not been explored. It has also not been assessed if the reference phylogeny can be deployed in conjunction with the reference alignment to improve alignment accuracy in this context.
  
  
  RESULTS
  We assess different strategies for short read alignment and propose a novel phylogeny-aware alignment procedure. Our alignment method can improve the accuracy of subsequent phylogenetic placement of the reads into a reference phylogeny by up to 5.8 times compared with phylogeny-agnostic methods. It can be deployed to align reads to alignments generated by using fundamentally different alignment strategies (e.g. PRANK(+F) versus MUSCLE).
  
  
  BACKGROUND
  http://www.exelixis-lab.org/software.html
authors.affiliation: The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, D-69118 Heidelberg, Germany. simon.berger@h-its.org
authors.forename: Simon A
authors.initials: SA
authors.lastname: Berger
authors.forename: Alexandros
authors.initials: A
authors.lastname: Stamatakis
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D016013:Likelihood Functions; D010802:Phylogeny; D012015:Reference Standards; D016415:Sequence Alignment / Q000379:methods*; D012984:Software