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

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.

global-alignment biopython

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updated 3.6 years ago by Istvan Albert 10K • | written 3.6 years ago by Fatemeh 0

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

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written 3.6 years ago by Joe 2.2K

1 answer

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

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written 3.6 years ago by Istvan Albert 10K

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