Multiple sequence alignment (MSA) is a cornerstone of computational biology, facilitating the exploration of functional, structural and evolutionary relationships among biological sequences.

Unfortunately, existing computer programs for sequence alignment are not based explicitly on detecting the homology of nucleotides, and so there is a notable gap in the existing bioinformatics ...

Multiple observations of homologous protein or nucleic acid sequences from different organisms are often available. But because mutations and sequence errors misalign these data, multiple sequence ...