HAL: A hierarchical format for storing and analyzing multiple genome alignments

Bioinformatics

Volumn 29, Issue 10, 2013, Pages 1341-1342

  Hickey, Glenn ^a   Paten, Benedict ^a   Earl, Dent ^a   Zerbino, Daniel ^a   Haussler, David ^a,b  

^a University of California Santa Cruz   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; ARTICLE; COMPUTER LANGUAGE; COMPUTER PROGRAM; EQUIPMENT; GENOME; GENOMICS; HUMAN; METHODOLOGY; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT;

ANIMALS; BASE SEQUENCE; EVOLUTION, MOLECULAR; GENOME; GENOMICS; HUMANS; PHYLOGENY; PROGRAMMING LANGUAGES; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 84877940570     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt128     Document Type: Article

References (8)

1. Blanchette, M. et al. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res., 14, 708-715.
2. Haussler, D. et al. (2009) Genome 10k: a proposal to obtain whole-genome sequence for 10 000 vertebrate species. J. Hered., 100, 659-674.
3. Neph, S. et al. (2012) Bedops: high-performance genomic feature operations. Bioinformatics, 28, 1919-1920.
4. Notredame, C. (2007) Recent evolutions of multiple sequence alignment algorithms. PLoS Comput. Biol., 3, e123.
5. Paten, B. et al. (2011) Cactus: algorithms for genome multiple sequence alignment. Genome Res., 21, 1512-1528.
6. Pevzner, P. and Tesler, G. (2003) Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Res., 13, 37-45.
7. Quinlan, A.R. and Hall, I.M. (2010) Bedtools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842.
8. The HDF5 Group. (2000-2010) Hierarchical data format version 5. http://www.hdfgroup.org/HDF5.