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:

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$ which anchorwave
/local/cluster/anchorwave/bin/anchorwave
$ anchorwave
Program anchorwave vRC3.0

help message:

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$ anchorwave
Program anchorwave vRC3.0
Usage: anchorwave <command> [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:

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/nfs1/CGRB/databases/software/anchorwave

software ref: https://github.com/baoxingsong/AnchorWave
research ref: Under preparation