COMBAT (COMBined AlignmenT) implements the combined DNA/protein alignment method described in Christian N. S. Pedersen, Rune B. Lyngsø and Jotun Hein. "Comparison of coding DNA" in Proceedings of the 9th Annual Symposium of Combinatorial Pattern Matching (CPM), 1998.

It is composed of 3 tools :
  ’combat’ takes as input two sequences, an amino-acid distance matrix, a nucleotide distance matrix and two affine gap functions (one for the amino-acid level and one for the nucleotide level) and produces an optimal alignment of the two sequences in the DNA/protein model with respect to these parameters.
  ’convert’ converts a similarity matrix into a distance matrix
  ’combine’ takes two sequences and an alignment generated by combat, and prints the alignment in the usual textual representation.

You will find more information about COMBAT here.