# Analysis

In the `mysim.yaml`

file you created you should see an analysis section. To
learn more about the available options, please see Configuration Options page. The analyses
can be ran using the command

```
webng analysis --opts mysim.yaml
```

and webng will run the analyses using the configuration options given by the file.

## Probability distribution analyses

### Average analysis

`average`

will create a N by N set of plots where N is the number of observables
you have in the BNG model after running the appropriate WESTPA tools. The results will
be saved in the folder written under `analyses/average/output`

(by default it is set
to `average.png`

). The plot will look like a matrix of plots where the diagonal
contains 1D probability distributions of each observable and every off-diagonal will be a
2D probability heatmap of each pair of observables. For various options available,
see Average page.

### Evolution analysis

The analysis `evolution`

will make a probability distribution evolution plot for
each observable so you can track the progress of your simulation. For various
options available, see Evolution page.

## Clustering and network analyses

### Clustering analysis

`cluster`

analysis will allow you to use the transition matrix estimated from your
simulation and do PCCA+ clustering.
This type of clustering is useful to maximize transition within stable states and minimize transitions
between unstable states and in this way it takes kinetics of the system into account. For various
options available, see Cluster page.

### Network generation

`network`

analysis will use the results of your clustering and give you `gml`

files
that can be used to visualize the clusters. This analysis will give you two files, one for the
full transition matrix and one for the clustered result. For various options available, see
Network page.