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hal website  

HAL is a structure to efficiently store and index multiple genome alignments and ancestral reconstructions. HAL is a graph-based representation which provides several advantages over matrix/block-based formats such as MAF, such as improved scalability and the ability to perform queries with respect to an arbitrary reference or subtree.

This package includes the HAL API and several analysis and conversion tools which are described below. HAL files are presently stored in either HDF5 or mmap format, but we note that the tools and most of the API are format-independent, so other databases could be implemented in the future.

Environment Modules

Run module spider hal to find out what environment modules are available for this application.

System Variables

  • HPC_HAL_DIR - installation directory
  • HPC_HAL_BIN - executable directory


If you publish research that uses hal you have to cite it as follows:

Glenn Hickey, Benedict Paten, Dent Earl, Daniel Zerbino, and David Haussler. HAL: A Hierarchical Format for Storing and Analyzing Multiple Genome Alignments. Bioinformatics. 2013. Advance Online Access