How to choose the key parameters during sequence assembly for Restriction site Associated DNA Sequencing (RADSeq) has been known to be important. Using parameters not suitable for a particular dataset could cause significant bias in downstream analyses, resulting in false conclusion. The conventional ways for solving this issue are usually centered around picking a set of parameter that optimizes certain metrics defined during the bioinformatic process (e.g., this paper). Here I work on a new method for determining the optimal parameters through a likelihood estimator based on the nucleotide diversity in the given dataset. Part of the result can be found in my published paper. You can also try out a Python script I wrote for this method.