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High quality sequence alignments of RNA and DNA sequences are a prerequisite for the comparative analysis of genomic sequence data. The high level of sequence heterogeneity, as compared to proteins, makes good alignments of nucleic acid sequences often impossible. In many cases, the nucleic acid sequences under consideration, or parts of them, code for proteins. While protein sequences can still show substantial homology, the corresponding nucleic acid sequences have already evolutionarily diverged, thus they are essentially randomized. This is caused by the inherent redundancy of the genetic code: Most amino acids have more than one codon on the level of nucleic acid. This specific problem leads to gaps and incorrectly aligned segments within coding regions. In the thesis a multiple nucleic acid alignment procedure was implemented that uses genetic information about coding and non-coding regions as part of the scoring function in order to improve the resulting alignment. Ou