Fast Algorithms for Inferring Evolutionary Trees

Fast Algorithms for Inferring Evolutionary Trees

We present algorithms for the perfect phylogeny problem restricted to binary characters. The first algorithm is faster than a previous algorithm by Gusfield when the input matrix for the problem is sparse. Next, we present two online algorithms. For the first of these, the set of species is fixed and the characters are given as input one at a time, while, for the second, the set of characters i...

Inferring Phylogenetic Trees Using Evolutionary Algorithms

We consider the problem of estimating the evolutionary history of a collection of organisms in terms of a phylogenetic tree. This is a hard combinatorial optimization problem for which different EA approaches are proposed and evaluated. Using two problem instances of different sizes, it is shown that an EA that directly encodes trees and uses ad-hoc operators performs better than several decode...

Fast Hashing Algorithms to Summarize Large Collections of Evolutionary Trees

Different phylogenetic methods often yield different inferred trees for the same set of organisms. Moreover, a single phylogenetic approach (such as a Bayesian analysis) can produce many trees. Consensus trees and topological distance matrices are often used to summarize the evolutionary relationships among the trees of interest. These summarization techniques are implemented in current phyloge...

Inferring Evolutionary Trees with Strong Combinatorial Evidence

We consider the problem of inferring the evolutionary tree of a set of n species. We propose a quartet reconstruction method which speci cally produces trees whose edges have strong combinatorial evidence. Let Q be a set of resolved quartets de ned on the studied species, the method computes the unique maximum subset Q∗ of Q which is equivalent to a tree and outputs the corresponding tree as an...

On the Complexity of Inferring Rooted Evolutionary Trees