Jun 272013
 

rRNA phylogeny

:: DESCRIPTION

rRNA phylogeny is a program package to phylogenetic analyses (using Phylip) of rRNA using a matrix of empirical substitution rates and the OTRNA model.

4to20 translates DNA/RNA sequences to rRNA-coded sequences in 20-letter code
20to4 translates rRNA-coded sequences to 4-letter code
nadist performs Distance analysis using the OTRNA model and gamma-distributed rates.
rRNAdist, rRNAml, rnaml: modified versions of protdist, protml, protmlk from PHYLIP to use the rRNA matrices.
etseqgen: modification of PSeq-gen to use the PMB model or the Bacterial SSU rRNA model.

::DEVELOPER

The Tillier Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 rRNA phylogeny

:: MORE INFORMATION

Citation:

Empirical substitution models for Ribosomal RNA
Andrew Smith, Thomas W. H. Lui and Elisabeth R. M. Tillier,
Mol Biol Evol (2004) 21: 419-427

High apparent rate of simultaneous compensatory base-pair substitutions in ribosomal RNA
Tillier, E. R. M. and R. A. Collins,
Genetics (1998) 148: 1993-2002

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