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I found the human genome alignment sets here: https://www.ensembl.org/info/genome/compara/multiple_genome_alignments.html

but they doesn't include, for example, ancient human genomes, e.g. those here: https://reich.hms.harvard.edu/allen-ancient-dna-resource-aadr-downloadable-genotypes-present-day-and-ancient-dna-data

or, for example, any of the other 'pan genome' whole genome alignments here: https://humanpangenome.org/

However, those latter two resources don't include whole genome alignments...

About 10 years ago I remember reading a paper that used 'lots' of genomes to uncover novel features using different patterns of conservation, demonstrating the power of the approach.

Have I missed a new, more up to date, whole genome alignment resource?

Many thanks,

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    $\begingroup$ This seems like it might be an XY problem. Can you please provide more context to your question and explain what you want to do with this resource? You're asking for a fairly large dataset, and there's probably a better way to do what you want without downloading all that data. $\endgroup$
    – gringer
    Oct 31, 2023 at 4:17

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The obvious thing missing from your list is the telomere-to-telomere genome assemblies that have been coming out in the last couple years.

Assembly link here.

There are now a few others as well that are similar.

It's been demonstrated that this T2T assembly improves mapping rates, in some cases pretty dramatically.

I am not sure entirely what you want from whole genome alignments, but UCSC if not others has incorporated the T2T assembly. Here is a related commentary (which I haven't read in any detail).

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