How can I retrieve H. sapiens neanderthalensis sequences from http://projects.ensembl.org/neandertal/?

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Pawel Buczkowicz

You can retrieve the data here (ftp://ftp.ebi.ac.uk/pub/databases/ensembl/neandertal/) as aligned BAM files. It contains a Neanderthal genome aligned to human genome and six human genomes.

Albino Bacolla

As Pawel mentioned, your work may require that you look at BAM files and see if your gene of interest is contained in those files.