Background: The neighbor-joining method by Saitou and Nei is a widely used method for constructing phylogenetic trees. The formulation of the method gives rise to a canonical (n3)...
The inference of evolutionary trees using approaches which attempt to solve the maximum parsimony (MP) and maximum likelihood (ML) optimization problems is a standard part of much...
Background: To understand the evolutionary role of Lateral Gene Transfer (LGT), accurate methods are needed to identify transferred genes and infer their timing of acquisition. Ph...
Sophie S. Abby, Eric Tannier, Manolo Gouy, Vincent...
Background: The Monte Carlo simulation of sequence evolution is routinely used to assess the performance of phylogenetic inference methods and sequence alignment algorithms. Progr...
Botond Sipos, Tim Massingham, Gregory E. Jordan, N...
Background: Applications of computational methods for predicting protein functional linkages are increasing. In recent years, several bacteria-specific methods for predicting link...
Anis Karimpour-Fard, Sonia M. Leach, Ryan T. Gill,...