Update file README.md

new_specie/README.md

-Scripts to train an auto-encoder and cluster animal vocalisations by frequency-contour similarity
+Scripts to train an auto-encoder and cluster animal vocalisations by frequency-contour similarity.
+
 Vocalisation detection needs to be done prior to this process (stored in a .csv file)
 
-Scripts need to be called in the following order :
-train_AE.py
-compute_embeddings.py
-sort_cluster.py
 
-use  `python myscript.py --help` to get more information on each scripts' usage
+
+###Scripts need to be called in the following order:
+
+If you want to train your own auto-encoder (optional since the generic one might suffice), use `python train_AE.py detections.csv`
+
+Use trained auto-encoder weights to project your vocalisations with `python compute_embeddings.py generic_embedder.weights detections.csv`
+
+Visualise vocalisation embeddings and resulting clusters with `python sort_cluster.py embeddings.npy detections.csv`
+
+use `python myscript.py --help` to get more information on each scripts' usage and options
 
 required packages can be install using  `pip install -r requirements.txt`