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baoxingsong / AnchorWave

Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation
MIT License
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Anchorwave ali documentation #27

Closed diego-rt closed 1 year ago

diego-rt commented 2 years ago

Hello,

I noticed that there is a function called 'ali' that is not documented. Is that a wrapper for WFA and can be used as such? The problem is that when I run it on two fasta files of the human and axolotl gene for SMAD1, I get the following output:

>SMAD1

>SMAD1
baoxingsong commented 2 years ago

Yes, that is a wrapper for 2 pieces affine gap cost WFA. Could you share your input files and commands please?