diff --git a/README.md b/README.md
index 2bdc9032071d0dd7682d3dd968ae2f85e2528c5a..0698a8d5afa1abf3027e2ac8b266212eed40d0ea 100644
--- a/README.md
+++ b/README.md
@@ -14,7 +14,7 @@ WARIO is a tool for the structural characterization of highly-flexible proteins.
 
 #### Running WARIO
 
-To run WARIO to characterize an ensemble, the user can directly execute the [contact_clustering](https://gitlab.laas.fr/moma/WARIO/-/blob/main/wario/contact_clustering.ipynb) notebook, which contains the detailed pipeline and allows a step-by-step implementation of the tool.
+To run WARIO to characterize an ensemble, the user can directly execute the [contact_clustering](https://gitlab.laas.fr/moma/methods/analysis/WARIO/-/blob/main/wario/contact_clustering.ipynb) notebook, which contains the detailed pipeline and allows a step-by-step implementation of the tool.
 
 #### The paper
 
@@ -38,16 +38,16 @@ wario-notebooks
 ```
 opens the ready-to-use jupyter notebook.
 
-The installation procedure works correctly with recent versions of Linux (Ubuntu 20.04 and 22.04) and MacOS (Sonoma 14.4.1) operating systems. Typical install time on a normal desktop computer is around 5 minutes. If you encounter any trouble to install WARIO, please file an [issue](https://gitlab.laas.fr/moma/WARIO/-/issues) or [contact us](mailto:javier.gonzalez-delgado@math.univ-toulouse.fr).
+The installation procedure works correctly with recent versions of Linux (Ubuntu 20.04 and 22.04) and MacOS (Sonoma 14.4.1) operating systems. Typical install time on a normal desktop computer is around 5 minutes. If you encounter any trouble to install WARIO, please file an [issue](https://gitlab.laas.fr/moma/methods/analysis/WARIO/-/issues) or [contact us](mailto:javier.gonzalez-delgado@math.univ-toulouse.fr).
 
 ## DEMO (data example)
 
-WARIO can be tested on the MD simulation of the P113 protein ensemble included [here](https://gitlab.laas.fr/moma/WARIO/-/blob/main/wario/P113). This dataset contains $n=100001$ conformations for a sequence of length $L=13$. To run WARIO on the P113 ensemble, the user can uncomment the lines
+WARIO can be tested on the MD simulation of the P113 protein ensemble included [here](https://gitlab.laas.fr/moma/methods/analysis/WARIO/-/tree/main/wario/P113). This dataset contains $n=100001$ conformations for a sequence of length $L=13$. To run WARIO on the P113 ensemble, the user can uncomment the lines
 
 ```
 #ensemble_folder = "/".join([path_to_notebook,'P113']) # Path to the folder containing trajectory files
 #ensemble_name = "P113" # Name the ensemble
 ```
-in the second code cell of the [contact_clustering](https://gitlab.laas.fr/moma/WARIO/-/blob/main/wario/contact_clustering.ipynb) notebook, and proceed following the usual guidelines. Then, results will be automatically saved in the [P113 folder](https://gitlab.laas.fr/moma/WARIO/-/blob/main/wario/P113). The typical running time for this data example is around 30 minutes in a normal desktop computer using 5 threads. 
+in the second code cell of the [contact_clustering](https://gitlab.laas.fr/moma/methods/analysis/WARIO/-/blob/main/wario/contact_clustering.ipynb) notebook, and proceed following the usual guidelines. Then, results will be automatically saved in the [P113 folder](https://gitlab.laas.fr/moma/methods/analysis/WARIO/-/tree/main/wario/P113). The typical running time for this data example is around 30 minutes in a normal desktop computer using 5 threads.