There are many ways in order to qualitatively identify a suspect in a crime. Besides the things that you have mentioned, there are other ways that police investigators use in order to determine a suspect. The determination of evidence in the crime scene can be used to identify any suspect in a crime.
Fingerprint is unique to every individual. No two individual have the same fingerprints - even identical twins. It can be used in order to determine if a person is in the crime scene. It may not directly tell whether the person is a suspect but it can be a lead in solving the case. DNA typing can be implemented if there are suspicious biological material present in the crime scene (e.g. hair stands, sperm, mucous, grafted skin, blood, etc...)
Interviews and psychological assessment can be used indirectly in order to determine whether an accused is telling the truth or not. Anything that the accused says can be used in the trial.