CHARACTER BASED TREES

Identify positions that best describe how characters (amino acids) are derived from common ancestors and operate directly on the aligned sequences using heuristic tree search algorithms.

These approaches often generate a starting tree using a fast algorithm and then perform local rearrangements - to improve the tree score.

For about 12 taxa or fewer, evaluate all possible trees exhaustively.

Seek the ‘most-parsimonious’ tree which requires the fewest number of evolutionary events (e.g., nucleotide substitutions, amino acid replacements) to explain the sequences.

MAXIMUM PARSIMONY

a character-based approach that infers a phylogenetic tree by minimizing the total number of evolutionary steps required to explain a given set of data assigned on the leaves

MAXIMUM LIKELIHOOD

An alternative to maximum parsimony. It is computationally intensive. A likelihood is calculated for the probability of each residue in an alignment, based upon some model of the substitution process.

A method of statistical inference in which Bayes' theorem is used to update the probability for a hypothesis as more evidence or information becomes available. Bayesian inference is an important technique in statistics, and especially in mathematical statistics.

BAYESIAN INFERENCE

Bayesian updating is particularly important in the dynamic analysis of a sequence of data. Bayesian inference has found application in a wide range of activities, including science, engineering, philosophy, medicine, sport, and law.

APPLICATION

Study tumor development

Reconstruction of evolutionary history

Study the evolutionary and epidemiological dynamics of pathogens