Perl scripts
(for Mac OS X, Unix and Linux)
| 2analysis.zip | Creates datfiles for use in MrBayes or Phase 2.0 including the secondary-strucure information from the annotation in the input file (a consensus secondary structure annotation sequence called "HELIX"). If the input is provided as *.mase-file, the definition of included sites chosen and saved with SEAVIEW can be added to the MrBayes-file. input-format |
| 2ct.zip | This
script converts a *.fasta or *.mase file to a *.ct-format as outputed by
mfold. It is possible to include pseudoknot structures (see
structure annotation), that are not predicted by mfold. This format can
be used to display structures in RnaViz2. input-format |
| ct2mase.zip | Converts
a *.ct file (one or multiple sequences) to Sequence plus structure
annotation in mase-format for SEAVIEW. It does not introduce special
characters for pseudoknots (mfold generated files will not include
pseudoknots, but be aware that *.ct-files from this site do!!!). input-format: ct-from mfold. |
| structure_consensus.zip | Calculates
a consensus structure from an alignment including: a) ONE Structure annotation ("HELIX",see input-format) or b) Structure annotations for EVERY sequence (HELIX_<corresponding sequence name>; see input-format). In case
a) it is also possible to extrapolate structures for all sequences
within the (provided and correct) alignment. A helix-numbering as
sequence called "Helixnr" can be present and will be ignored. |
| basefreqs.zip | Calculation of sequence lengths and base composition of all sequences in an alignment. |
| seq_consensus.zip | Calculation of consensus sequences. Shows small letters for positions with gaps above the consensus level. |