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New Alignment Methods Needed. Anyone?

Thomas Mailund is working on a project right now where he’s analyzing a whole-genome alignment of human, chimp, orangutan, and macaque. While his current method -- downloading the alignment from the UCSC genome browser in the MAF format and using the bx-python module from Penn State to analyze it -- is good enough for scanning large chunks, he needs something more refined to probe specific regions in more depth. Anyone got any suggestions?