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The exact problem you're running into (pitch doubling/halving) with Praat is well-known, and that can easily be fixed on a per-speaker basis by tweaking the floor and ceiling settings. You should also be able to use a Praat script for pulling out the vowels as well (if you're just looking at segmentation, maybe there's something else you need Allosaurus for). Though, if you're looking at other tools and have... Source: about 1 year ago
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