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Note: Compatibility issues with Maq 0.7.1 and Maqview 0.2.3 have been experienced. So, use Maq 0.6.6 and maqview 0.2.3 together.

With a reference file ref.bfa and an maq alignment file out.map :

maq assemble -s out.cns ref.bfa out.map

maqindex -i -c out.cns out.map chr1   (here chr1 is just a header of one of the sequences in the ref.bfa file)

maqview -c out.cns out.map  (needs X terminal to work)

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