[amelius]

And the compressor does not think: "how can I make these two sequences align better without wasting a lot of space?"

[ebolyen]

No, because alignment, in the general case, is O(n^2). It is ironically one of the more tractable and well solved problems in bioinformatics.

[tiagod]

The compressor doesn't think about anything. Also, Zstd doesn't have the goal of reaching the highest possible compression ratio. It's more geared toward lowest overhead, high bandwidth compress/decompress.