Background: Proteins that evolve from a common ancestor can change functionality over time, and it is important to be able identify residues that cause this change. In this paper ...
Background: Distance-based methods are popular for reconstructing evolutionary trees thanks to their speed and generality. A number of methods exist for estimating distances from ...
The multiple species de novo gene prediction problem can be stated as follows: given an alignment of genomic sequences from two or more organisms, predict the location and structur...
Conventional phylogenetic tree estimation methods assume that all sites in a DNA multiple alignment have the same evolutionary history. This assumption is violated in data sets fro...
Background: Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. Howeve...
Paolo Ferragina, Raffaele Giancarlo, Valentina Gre...