Viral Genome Alignment in MAFFT
Hi! I want to do an alignment for 743 viral genomes (27-30 kb approximately) in MAFFT. All genomes are complete and downloaded from NCBI virus. I want to do the best alignment and have already performed 5 test alignments, but I need your suggestions and experience to get the best possible result.
What parameter do you suggest to use for a case like this? Thank you!
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mauricio.1313 •
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If these virii are closely related then you should be fine using default settings. Depending on alignment you get some manual editing may be warranted afterwards.