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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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no species name in MAF output #35

Closed leejimmy93 closed 2 years ago

leejimmy93 commented 2 years ago

Thanks for developing such a nice tool! I am checking the MAF output from anchorwave and noticed that there is no species name in the MAF file, however tools like MafFilter requires that. Is it possible to include species name in the MAF output or do you have recommendation of other tools other than MafFilter to post process MAF file? Also, I could not find explanations about the difference between .f.maf and .maf, is .maf just concatenated file of .f.maf? Thank you again! really nice tool!

baoxingsong commented 2 years ago

At the first version, we had species name. While under the suggestions from other users, we removed that. Could your use some linux tools, i.e. awk to add species names? Yes, .maf is just the concatenated file of .f.maf.

leejimmy93 commented 2 years ago

I see, thanks for the reply!