Codaln
Alignments of Nucleic Acid Sequences
Codaln (Stocsits et al., 2005), (Stocsits, 2003) produces multiple nucleic acid alignments using information on coding and non-coding regions as part of the scoring function. This is done in order to prevent the problem of higher sequence divergency on the level of nucleic acids as compared to the underlying protein sequences in the case of coding at a certain region of the input nucleic acid sequences.