Here's the UCSC Genome Browser page for the Neandertal genome. Ensembl is supposed to have something up soon, but I don't see it. Here's the Anfo Short Read Aligner/Mapper; you can download it on that page. Page 21 of the online supplement has some configuration file code on it which might be useful. Also, make sure to check out the supplements.
Neandertal online
Explore the Neandertal genome on UCSC Genome Browser and discover valuable resources like the Anfo Short Read Aligner.
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