One of the core classical problems in computational biology is that of constructing the most parsimonious phylogenetic tree interpreting an input set of sequences from the genomes of evolutionarily related organisms. We reexamine the classical maximum parsimony (MP) optimization problem for the general (asymmetric) scoring matrix case, where rooted phylogenies are implied, and analyze the worst...

Maximum parsimony and maximum likelihood are two contrasting approaches for reconstructing phylogenetic trees from sequence and character data. We establish analytic links between these methods (extending connections reported earlier) under the simple Poisson model of substitutions in two settings. First, we show that if the underlying state space is sufficiently large then the maximum likeliho...

In this paper we investigate mathematical questions concerning the reliability (reconstruction accuracy) of Fitch's maximum parsimony algorithm for reconstructing the ancestral state given a phylogenetic tree and a character. In particular, we consider the question whether the maximum parsimony method applied to a subset of taxa can reconstruct the ancestral state of the root more accurately th...

The Maximum Parsimony (MP) problem aims at reconstructing a phylogenetic tree from DNA sequences while minimizing the total number of genetic transformations. In this paper we propose a carefully devised simulated annealing implementation, called SAMPARS (Simulated Annealing for Maximum PARSimony), for finding near-optimal solutions for the MP problem. Different possibilities for its key compon...

The similarity of the molecular matter of the organisms on Earth suggest that they all share a common ancestor. Thus any set of species is related, and this relationship is called a phylogeny. The links (or evolutionary relationships) among a set of organisms (or taxa) form a phylogenetic tree, where modern organisms are placed at the leaves and ancestral organisms occupy internal nodes, with t...

Four local search algorithms are investigated for the phylogenetic tree reconstruction problem under the Maximum Parsimony criterion. A new subtree swapping neighborhood is introduced and studied in combination with an effective array-based tree representation. Computational results are shown on a set of randomly generated benchmark instances as well as on 8 real problems (sequences of phytopat...