title: HAL: a hierarchical format for storing and analyzing multiple genome alignments.
abstract: BACKGROUND
  Large multiple genome alignments and inferred ancestral genomes are ideal resources for comparative studies of molecular evolution, and advances in sequencing and computing technology are making them increasingly obtainable. These structures can provide a rich understanding of the genetic relationships between all subsets of species they contain. Current formats for storing genomic alignments, such as XMFA and MAF, are all indexed or ordered using a single reference genome, however, which limits the information that can be queried with respect to other species and clades. This loss of information grows with the number of species under comparison, as well as their phylogenetic distance.
  
  
  RESULTS
  We present HAL, a compressed, graph-based hierarchical alignment format for storing multiple genome alignments and ancestral reconstructions. HAL graphs are indexed on all genomes they contain. Furthermore, they are organized phylogenetically, which allows for modular and parallel access to arbitrary subclades without fragmentation because of rearrangements that have occurred in other lineages. HAL graphs can be created or read with a comprehensive C++ API. A set of tools is also provided to perform basic operations, such as importing and exporting data, identifying mutations and coordinate mapping (liftover).
  
  
  BACKGROUND
  All documentation and source code for the HAL API and tools are freely available at http://github.com/glennhickey/hal.
  
  
  BACKGROUND
  hickey@soe.ucsc.edu or haussler@soe.ucsc.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz CA 95064, USA. hickey@soe.ucsc.edu
authors.forename: Glenn
authors.initials: G
authors.lastname: Hickey
authors.forename: Benedict
authors.initials: B
authors.lastname: Paten
authors.forename: Dent
authors.initials: D
authors.lastname: Earl
authors.forename: Daniel
authors.initials: D
authors.lastname: Zerbino
authors.forename: David
authors.initials: D
authors.lastname: Haussler
mesh_terms: D000818:Animals; D001483:Base Sequence; D019143:Evolution, Molecular; D016678:Genome; D023281:Genomics / Q000379:methods; D006801:Humans; D010802:Phylogeny; D011381:Programming Languages; D016415:Sequence Alignment / Q000295:instrumentation / Q000379:methods*; D012984:Software