Over the weekend I was reading Neanderthal Man by Svante Paabo . This book discusses comparative genomics of humans and close relatives, including the complete genome of Pan paniscus published in Nature in 2012, and the complete genome of an Altai Neanderthal in 2014. It is clear from the phylogenetic trees and other comparisons in these papers that the complete genomes can be analyzed, for example to show diversity within the Major Histocompatibility Complex in comparison to diversity in other regions of the genomes.
However, when I attempt to download the MHC region from each of the genomes to do some of my own comparisons, I find that it is not easy to get the data. The genomes are not well assembled and annotated on the public sites, so I cannot just search for the MHC gene region in Pan troglodytes, Altai Neanderthal genome, or Pan paniscus genome.
Does anyone here know if the annotated genomes are available at some other site? Papers discussing the genomes seem to indicate that the authors have access to annotation to determine which genes and gene families are shared between modern humans and Neanderthals.