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

Abstract
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:
 


    Input:
            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

    Output:
            Coded rrna alignment in both fasta and phylip format
 

    Input:
        rRNA coded sequences in fasta or phylip format

    Output:
        dna sequences in phylip format
 

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

    Output:
        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)