MSA INDEL Realigner

Question

[Coryza]

Hi all,

Does someone know if there's a tool that is able to realign INDELs based on MSA (preferably clustalw/clustalo) output; similar as to what GATK does on BAM files?

Thanks!

Answer 1

[h.mon]

Mafft has an option to realign particular regions, but I don't how it will perform at realigning indels.

[Coryza]

Hi - I've looked into your suggestions and it seems that it's exactly doing as how I would want it to do.