Traditional paternity testing relies on comparing at specific locations (loci) on nuclear DNA. However, "alternative methods" typically address scenarios where the alleged father is unavailable or the standard nuclear DNA is highly degraded. 1. Y-Chromosome (Y-STR) Analysis
In some contexts, identification may rely on "comparative methods" if biological material is insufficient: An Alternative Method of Identification of a Fa...
Introduction - DNA Technology in Forensic Science - NCBI Bookshelf An Alternative Method of Identification of a Fa...