Provided herein are methods and apparatuses for analyzing a patient's dental arches in order to generate a treatment plan for the dentition. In particular described herein are methods and apparatuses for analyzing a patient's dental arches when the patient is missing one or more teeth. Methods and apparatuses are provided to properly number the teeth of a patient's arches after a dental scan, including automatically detect missing teeth after a dental scan and estimating the dimensions of the missing teeth. Methods and apparatuses are provided to perform an analysis of the patient's arches that uses the estimated dimensions of the missing teeth. Methods and apparatuses for designing and manufacturing the aligner are also provided.
