Obviously the pitch correction part should be seen as a "last resort", to use only if you notice, before starting the mixing phase, that there are some errors that cannot be recorded again, but that at the same time are too big to not be noticed, and that risk to ruin the song.
First off let's say that auto tuning tools works fine only with clean, monophonic sounds: any kind of background noise, or rasp vocals, or distorted sound may be misinterpreted by the algorithm and lead to mistakes. It's also suggestable to process the vocal parts without sibilant letters (s), and the guitar - bass parts where there are no slides-bendings.
There are two types of autotuning tools:
1) Automated Pitch Correctors: These are the kind of tools, such as Antares Autotune, or the free Gsnap and Kerovee, where you can choose the key of the song and other parameters, and let the plugin to automatically slide the wave on the piano roll, in order to match in real time the scale used on the song. It's a good thing not to leave it activated for the whole song, but to Automate it in order to be switched on only when needed, and turned off when unnecessary. It is also possible to create a MIDI track and route the plugin on it in order to manually decide the pitch as it was a regular synth, in facts today the industry standard is using Autotune manually, line by line, in Graphic Mode.
In conclusion, regardless to the kind of plugin you may choose, autotuning should be used with extreme caution, only when impossible to record again, and only for the single parts that really needs it, since often is better to hear a more natural interpretation, although not perfectly in tune, than the "Midi-sounding" voice that sometimes can be heard, even on commercial songs. The risk is to have a completely flattened and lifeless voice, altough perfectly in tune :)
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