A global maximum likelihood super-quartet phylogeny method

Abstract

Extending the idea of our previous algorithm [17, 18] we developed a new sequential quartet-based phylogenetic tree construction method. This new algorithm reconstructs the phylogenetic tree iteratively by examining at each merge step every possible super-quartet which is formed by four subtrees instead of simple quartet in our previous algorithm. Because our new algorithm evaluates super-quartet trees, each of which may consist of more than four molecular sequences, it can effectively alleviate a traditional, but important problem of quartet errors encountered in the quartetbased methods. Experiment results show that our newly proposed algorithm is capable of achieving very high accuracy and solid consistency in reconstructing the phylogenetic trees on different sets of synthetic DNA data under various evolution circumstances.