This is the command mauveAlignment2anchors.pl that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
mauveAlignment2anchors - converts a Mauve alignment into Murasaki anchor format based on
gapped alignment data (each gap triggers a new anchor). Note this refers to the Mauve
alignment format, not the LAGAN .alignment file that Mauve also outputs.
mauveAlignment2anchors <input> [output]
--autoout -- create output file name automatically (on by default)
--noautoout -- disable the above "autoout" option
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