Here are the genome alignments resulting from "Split-alignment of genomes finds orthologies more accurately", Genome Biology 2015, 16:106. In the terminology of that paper, these are 2-split, post-masked alignments. They are in MAF format (http://genome.ucsc.edu/FAQ/FAQformat.html), with "p" lines (http://last.cbrc.jp/doc/last-split.html). Alignments with high ambiguity have not been removed, so if you want unambiguously 1-to-1 alignments, remove those annotated with mismap > 0.00001 or so. The chimp and orangutan alignments were made using the 500/30 gap costs suggested at the end of the paper.