Dependency Publisher's description
from M. Tillier
4to20 translates DNA/RNA sequences to rRNA-coded sequences in 20-letter code
* 4to20 translates DNA/RNA sequences to rRNA-coded sequences in 20-letter code
o rRNA structure in .bpseq format (see Comparative RNA Web Site for details)
o rRNA alignment in fasta format
the first sequence should be that of the corresponding .bpseq structure file
o Coded rRNA alignment in both fasta and phylip formats.
* 20to4 translates rRNA-coded sequences to 4-letter code
o rRNA-coded sequences in fasta or phylip format
o dna sequences in phylip format
* rnadist performs Distance analysis using the OTRNA model and gamma-distributed rates.
o coded rRNA sequences file in fasta format
o Gamma parameters for single-stranded sites and for double-stranded sites (enter 0 for equal rates)
o Distance matrices (opper 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
* 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.
o tree file
o choose PMB or RNA for substitution model (default is PMB)
o protein sequences or coded rRNA sequences in fasta format
System Requirements:No special requirements.
Program Release Status: New Release
Program Install Support: Install and Uninstall