Here’s the . is supposed to have something up soon, but I don’t see it. Here’s the ; you can download it on that page. Page 21 of the online supplement on it which might be useful.
URL: http://genome.ucsc.edu/Neandertal/
(2) Ensembl
URL: http://uswest.ensembl.org/index.html
(3) Anfo Short Read Aligner/Mapper
URL: http://bioinf.eva.mpg.de/anfo/
(4) has some configuration file code
URL: http://www.sciencemag.org/cgi/data/328/5979/710/DC1/1
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