Abstract
A phylogenetic tree estimates the “historical” connections between species or genes that they carry. Given a distance matrix from a set of objects, a phylogenetic tree is a tree whose nodes are the objects in the set and such that the distance between two nodes in the tree corresponds to the distance in the matrix. However, if the tree structure does not match the data perfectly then new nodes in the graph may be introduced. Such nodes may suggest “ancestral living beings” that can be used for phylogeny reconstruction. In general, finding these ancestral nodes on a phylogenetic graph is a difficult problem in computation and no efficient algorithms are known. In this paper we present an efficient algorithm to compute unknown nodes in phylogenetic trees when the similarity distance can be reduced to the L 1 metric. In addition, we present necessary conditions to be fulfilled by unknown nodes in general phylogenetic graphs that are useful for computing the ancestral nodes.
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