@@ -13,9 +13,9 @@ Besides this stand-alone version, a web server is freely available on the [EvryR
Installation
------------
If all the dependencies are already installed on your system, a simple `make` within the C-RCPred directory is sufficient to build the executable file.
If all the dependencies are already installed on your system, using the `make` command within the C-RCPred directory is sufficient to build the executable file.
Alternatively, C-RCPred can easily be installed by using Docker as follows:
@@ -52,20 +52,20 @@ The same test can be performed with the files provided for PDB_00805.
The following list of options can also be accessed by running `./C-RCPred`:
```
-f input fasta file
-s input secondary structure files,
-i input interaction secondary structure files,
-c constraint files where constraints are in the same order than the secondary structure and interaction files
-p probing data file for each RNA, in the same order than the fasta files (if no data for an RNA, an empty file is needed)
-o format of output "d" (dot-parenthesis, default), "j" (json) or "b" (base pair list format)
-e energy model (0: No energy model (use energies computed by upstream tools)), (1: ViennaRNA package model, default), (2: NUPACK model)
-t threshold for compatibility RNA (0->100, default 100)
-l lower probing threshold (0->100, if not specified, probing values between 0% and the upper threshold once normalized will not be taken into account)
-u upper probing threshold (0->100, if not specified, probing values between the lower threshold and 100% once normalized will not be taken into account)
-g output graph file
-k output cliques predicted
-q output cliques predicted without duplicates
-m maximum number of structures to output
-f Input fasta file
-s Input secondary structure files,
-i Input interaction secondary structure files,
-c Constraint files where constraints are in the same order than the secondary structure and interaction files
-p Probing data file for each RNA, in the same order than the fasta files (if no data for an RNA, an empty file is needed)
-o Format of output "d" (dot-parenthesis, default), "j" (json) or "b" (base pair list format)
-e Energy model (0: No energy model (use energies computed by upstream tools)), (1: ViennaRNA package model, default), (2: NUPACK model)
-t Threshold for compatibility RNA (0->100, default 100)
-l Lower probing threshold (0->100, if not specified, probing values between 0% and the upper threshold once normalized will not be taken into account)
-u Upper probing threshold (0->100, if not specified, probing values between the lower threshold and 100% once normalized will not be taken into account)