There was work done on evolutionary rates relative to phylogenetic trees,
tested on 16S rRNA done at the University of Illinois (Urbana) by
Gary Olsen and his co-workers. (gary at phylo.life.uiuc.edu) As far as I know it
hasn't been published, but I worked on it between 1993-1994.
The program FastDNAml (an updated version of Joseph Felsenstein's DNAml)
allows evolutionary rates as a parameter in the analysis of aligned DNA
sequences. The C source code is available by anonymous FTP from the Ribosomal
Database Project at info.mcs.anl.gov in directory pub/RDP/programs/fastDNAml.
Some other programs are described in: