When you use a computer to analyze data it has to be coded in a form that the computer can understand. This is where personal bias and circular reasoning starts: not in the analysis, in the coding.
Coding a Character State Matrix
Cladistics and Circular Reasoning
Despite the rigorous application of philosophical ploys to guard against circular reasoning in cladistic analysis it's a poster boy for circular reasoning because it's based in a paradigm which is the result of personal bias.
Archaeopteris
We're critical of the philosophical construction of the scientific method because it's been meticulously crafted to exclude any possibility that the truth can be either an acceptable premise, or a possible conclusion.