# Anchorwave vRC3 ## AnchorWave (Anchored Wavefront Alignment) 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. Location and version: ```console $ which anchorwave /local/cluster/anchorwave/bin/anchorwave $ anchorwave Program anchorwave vRC3.0 ``` help message: ```console $ anchorwave Program anchorwave vRC3.0 Usage: anchorwave [options] Commands: gff2seq get the longest full-length CDS for each gene genoAli whole chromosome global alignment and variant calling proali genome alignment with relocation variation, chromosome fusion or whole genome duplication ``` This software has been tested and the output for the test is here: ```console /nfs1/CGRB/databases/software/anchorwave ``` software ref: research ref: Under preparation