WHAM specifications


Unique identifier OMICS_00697
Alternative name Wisconsin’s High-throughput Alignment Method
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A set of query sequences of equal length, a database of reference sequence(s), and an error model.
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Jignesh M. Patel
  • person_outline Yinan Li
  • person_outline Allison Terrell

Additional information


Publication for Wisconsin’s High-throughput Alignment Method

WHAM citation


A hybrid short read mapping accelerator

BMC Bioinformatics
PMCID: 3598928
PMID: 23441908
DOI: 10.1186/1471-2105-14-67

[…] res for each base. ZOOM [] uses “spaced-seeds” in order to improve sensitivity. SHRiMP [] combines the spaced seeds and the Smith-Waterman algorithm to align reads with even higher sensitivity. SOAP, WHAM, BFAST, and GASSST apply the second approach to conduct the alignment computation. SOAP [] uses seeds (consecutive bases) and a hash lookup table algorithm to accelerate the alignment and is effi […]

WHAM institution(s)
University of Wisconsin–Madison, Madison, WI, USA
WHAM funding source(s)
Supported in part by a grant from the National Science Foundation under grant DBI-0926269.

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