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Welcome to the Maligner Wiki!

For installation instructions, see the README.

Be sure to check out the example script for aligning an in silico digest of an E. coli K-12 assembly to an in silico digest of the E. coli K-12 reference for an example of running maligner_dp.

We also have wiki pages for:

• Command Line Reference
• Input and Output Files - for documentation on input maps file format and the output alignment file format