Empirical substitution models for Ribosomal RNA.
        Andrew Smith, Thomas W. H. Lui and  Elisabeth R. M. Tillier

Full Text
Correct figure 4:  fig4.pdf

Programs download:

    All executables for Dos/Windows: rRNA_dos.zip

    All sources  for UNIX/LINUX: rRNA_unix.tar.Z

    Rate matrices: matrices.tar.Z

Please email  e.tillier@utoronto.ca for help/questions/bug reports.

Description of programs:

            rrna structure (.bpseq format, see Comparative RNA Web Site for details)
            rrna alignment in fasta format - First sequence should be that of the corresponding
                                                             .bpseq structure file

            Coded rrna alignment in both fasta and phylip format

        rRNA coded sequences in fasta or phylip format

        dna sequences in phylip format

        Coded rRNA sequences file in fasta format
        Gamma parameters for single-stranded sites and for double-stranded sites
            (enter 0 for equal rates)

        Distance matrices (Upper triangular) include:
            Ks.txt for single stranded sites only - Kimura (1981)  model
            Kd.txt for double stranded sites only - OTRNA model
            KsKd.txt for both  - Weighted average

    Modified versions of protdist, protml, protmlk from PHYLIP to use the rRNA matrices)