Update README.md

@@ -13,9 +13,9 @@ Besides this stand-alone version, a web server is freely available on the [EvryR
 
 
 Installation
 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:
 Alternatively, C-RCPred can easily be installed by using Docker as follows:
-```bash
+```
 git clone https://forge.ibisc.univ-evry.fr/EvryRNA/C-RCPred.git
 git clone https://forge.ibisc.univ-evry.fr/EvryRNA/C-RCPred.git
 cd C-RCPred
 cd C-RCPred
 docker build -t c-rcpred ./
 docker build -t c-rcpred ./
@@ -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`:
 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)
+ -g       Output graph file
+ -k       Output cliques predicted
+ -q       Output cliques predicted without duplicates
+ -m       Maximum number of structures to output
 ```
 ```
 
 
 Contact
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