Breakpoint phylogenies methods have been shown to be an effective way to extract phylogenetic information from gene order data. Currently, the only practical breakpoint phylogeny a...
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)...
Background: We present a novel method to encode ambiguously aligned regions in fixed multiple sequence alignments by ‘Pairwise Identity and Cost Scores Ordination’ (PICS-Ord)....
Robert K. Luecking, Brendan P. Hodkinson, Alexandr...
We describe a method for finding ungapped conserved words in rRNA sequences that is effective, utilizes evolutionary information and does not depend on multiple sequence alignment...
Liaofu Luo, Li-Ching Hsieh, Fengmin Ji, Mengwen Ji...
Background: Overlapping genes (OGs) in bacterial genomes are pairs of adjacent genes of which the coding sequences overlap partly or entirely. With the rapid accumulation of seque...