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anchorwave website  

AnchorWave (Anchored Wavefront Alignment) identifies collinear regions via conserved anchors (full-length CDS and full-length exon have been implemented currently) and breaks collinear regions into shorter fragments, i.e., anchor and inter-anchor intervals. By performing sensitive sequence alignment for each shorter interval via a 2-piece affine gap cost strategy and merging them together, AnchorWave generates a whole-genome alignment for each collinear block. AnchorWave implements commands to guide collinear block identification with or without chromosomal rearrangements and provides options to use known polyploidy levels or whole-genome duplications to inform alignment.

Environment Modules

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

System Variables

  • HPC_ANCHORWAVE_DIR - installation directory
  • HPC_ANCHORWAVE_BIN - executable directory


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

Baoxing Song, Santiago Marco-Sola, Miquel Moreto, Lynn Johnson, Edward S. Buckler, Michelle C. Stitzer. AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication. Proceedings of the National Academy of Sciences Jan 2022, 119 (1) e2113075119; DOI: 10.1073/pnas.2113075119