Phylogenetic trees generated by computational phylogenetics can be either rooted or unrooted depending on the input data and the algorithm used. A rooted tree is a directed graph that explicitly identifies a most recent common ancestor

Distance-matrix methods of phylogenetic analysis explicitly rely on a measure of "genetic distance" between the sequences being classified, and therefore, they require an MSA as an input. Distance is often defined as the fraction of mismatches at aligned

The maximum likelihood method uses standard statistical techniques for inferring probability distributions to assign probabilities to particular possible phylogenetic trees. The

Molecular phylogenetics methods rely on a defined substitution model that encodes a hypothesis about the relative rates of mutation at various sites along the gene or amino acid sequences

Morphological analysis
The basic problem in morphological phylogenetics is the assembly of a matrix representing a mapping from each of the taxa being compared to representative measurements for each of the phenotypic characteristics being used

Maximum parsimony (MP) is a method of identifying the potential phylogenetic tree that requires the smallest total number of evolutionary events to explain the observed sequence data. Some ways of scoring trees also include a "cost" associated with particular types of

Bayesian inference can be used to produce phylogenetic trees in a manner closely related to the maximum likelihood methods. Bayesian methods assume a prior