Performance study of supertree methods

INTRODUCTION Phylogenetic trees depict the relationships among varying species [1]. A simple example of this is a family tree. When referring to Figure 1, the three most important components of a tree include: the Node(s) (denoted by squares), the Branches (denoted by lines), and the Tips (denoted by circles). The Nodes represent the hypothetical ancestors. The Branches represent the evolution of a lineage. Lastly, the Tips represent the species being studied. Most phylogenetic trees are estimated from DNA sequence data. A supertree is a phylogenetic tree estimate which is produced by merging smaller phylogenetic tree estimates together [2-4]. By combining several phylogenetic trees together, we can gain a better understanding of how species are related to one another. One example would be combining the human and primate phylogenetic trees. MRP works by translating each branch of each individual tree into a matrix column; this process is repeated until a character matrix is formed [5,6]. All taxa that descend from the branch are represented in the matrix with a ‘1’, other taxa that are found in the tree are represented with a ‘0’, and taxa that aren’t found in the tree are represented with the missing data symbol ‘?’. Each branch of each input tree is encoded as a series of columns. Once complete, the character matrix includes all of the phylogenetic relationships contained in the source trees. The supertree is estimated from this Q&A