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)