# 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 <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:

```console
/nfs1/CGRB/databases/software/anchorwave
```

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