codaln 1.0 / code2aln 1.2
codaln is the successor of code2aln.codaln 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. The program allows plenty of user intervention to overrule the defaults.
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Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences
Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried, Peter F. Stadler
BMC Bioinformatics 6: 160 [epub] (2005)