Do we have any global pairwise alignment tool from biopython that uses bandsize ?

Question

[Fatemeh]

I have a huge list of genomes with length of about 30000. and I am going to calculate the distance matrix for it. So it would be computationally expensive so I want to use a band for that. I could not found any function in biopython. any help would be appreciated.

[Joe]

Just use kmer or mash distances. Aligning them is a futile endeavour.

Answer 1

[Istvan Albert]

I doubt that banding would help that much (even if it were implemented in Biopython, which I don't think it is)

You should use a tool designed to quickly align (similar) sequences, like MAFFT

https://mafft.cbrc.jp/alignment/software/algorithms/algorithms.html