Please fill out the submission form and click the Submit button. Input fields marked with a * are required.
(Load Example Data: toy example)

1st Multiple Sequence Alignment* 2nd Multiple Sequence Alignment*
This is the first alignment in FASTA format.
 This is the second alignment in FASTA format.
Enter alignment: Enter alignment:
or upload the alignment file: or upload the alignment file:
Phylogenetic Tree
Calculate the score for a given tree in Newick format. [?]
RNA secondary structure of duplex
Calculates score for given duplex structure in dot-bracket notation. [?]
Step 1 constraints intra-molecular structures marked as '(' and ')' and step 2 inter-molecular structure marked as '[' and ']'. Both structures have to be concatenated by '&'.
1st RNA secondary structure 2nd RNA secondary structure
Intra-molecular structure of the first alignment
in dot-bracket notation. [?]		 Intra-molecular structure of the second alignment
in dot-bracket notation. [?]
 

Options

Maximal percentage of gaps in alignment column [?]
Intra-molecular base paired reliability threshold
for accessibility (Delta)		 [?]
Minimal partial structure probability (Gamma) [?]
Constraint stems get extended by inner and outer base pairs [?]
Reliability threshold of evolutionary constrained base pairs [?]
Reliability threshold of evolutionary constrained unpaired bases [?]
Weighting factor for single stranded probabilities (Alpha) [?]
Weighting factor for thermodynamic overlap (Beta) [?]

Job Options

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