13 November 2003
We present examples using mRNA sequences from mouse and rat: three cytochromes and two zinc finger proteins. The underlying evolutionary model is derived from one proposed by Thorne, Kishino, and Felsenstein and improved by Hein and others. The demonstration implementation aligns two sequences using time and memory quadratic in the mean sequence length.
The algorithm is extensible, after Lunter, Miklós, Song and Hein
to multiple sequences. We mention a basic method to reduce time
and memory demands.