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RNAstat is a program written in
C++ designed to calculate nucleotide statistics, convert original RNA
sequences into a secondary structure coded dataset, generate consensus
sequence from an alignment and convert sequences from an alignment into
dot-bracket RNA structure format.
Start program and input files
Sequence statistics
Secondary structure statistics, sequence coding and dot-bracket structure format
Consensus sequence
Download RNAstat beta version for Windows
Download RNAstat file code
Reference: Subbotin, S.A.,
Sturhan, D., Vovlas, N., Castillo, P., Tanyi Tambe, J., Moens, M. and
Baldwin, J.G. (2006). Application of secondary structure model of rRNA
for phylogeny: D2-D3 expansion segments of the LSU gene of plant-parasitic
nematodes from the family Hoplolaimidae Filipjev, 1934. Molecular
Phylogenetics and Evolution 43: 881-890.
Acknowledgements. The support from the US National Science
Foundation grant DEB 0228692 and USDA grant 2005-00903 are acknowledged.
SECconverter is a program written in C++ designed to
convert dot-bracket RNA structure format into MrBayes command block with
stem and loop partitions under the complex model.
Program description:
- Start program and input files
- Output files
Download SECconverter beta version for Windows
Download SECconverter file code
Reference: Vovlas,
N., Subbotin, S.A., Troccoli, A., Liebanas, G. and Castillo, P.
(2008). Description and molecular characterisation of Rotylenchus
montanus sp. n. and recognition of R. jaeni comb. n. as a
separate species with approaches to molecular phylogeny of the genus
Rotylenchus (Nematoda, Tylenchida). Zooligica Scripta 37: 521-537.
Acknowledgements. The support from the US National
Science Foundation PEET grant DEB 0731516 is acknowledged.
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