Aligning multiple DNA or protein sequences is a fundamental step in the analyses of phylogeny, homology and molecular structure. Heuristic algorithms are applied because optimal mu...
When aligning biological sequences, the choice of scoring scheme is critical. Even small changes in gap penalties, for example, can yield radically different alignments. A rigorous...
Background: Phylogenetic analysis can be used to divide a protein family into subfamilies in the absence of experimental information. Most phylogenetic analysis methods utilize mu...
A progressive alignment algorithm produces a multi-alignment of a set of sequences by repeatedly aligning pairs of sequences and/or previously generated alignments. We describe a ...
Background: Determining beforehand specific positions to align (anchor points) has proved valuable for the accuracy of automated multiple sequence alignment (MSA) software. This f...