Manga Studio 4 works well at super high resolutions like 1200 dpi with aliased lines. Manga Studio 5 works optimally at slightly lower resolutions with anti-aliased lines by default.
Anti-aliasing may make lines look good on screen, but you’re actually better off with high resolution, jagged lines for print reproduction.
There is a setting in Manga Studio 4 that will smooth and anti-alias the display of lines on your canvas without actually producing anti-aliased lines here: See the check box labeled view quality at the top? I keep mine set to default because, after working with the app sine 2006, I’m just used to it.