I would like to be able to replicate what Galaxy does to find indels on my own machine. However, I am facing the following challenges:

1. I want to find Indels in the 3-way multiz alignment of hg18, panTro2, and rheMac2, but I cannot find the alignment anywhere. Where can I get the alignment file?

2. I cannot find code for extracting the Indel's anywhere. What program did you use?

Thanks so much!

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