There is a lot of literature available on Cluster Analysis [1,2]. Based on your data and the specific task that you intend to achieve, you can use one of the existing cluster analysis techniques (Eg: Hierarchical clustering, Centroid-based clustering, Distribution-based, Density based etc.).
Apart from using the right clustering technique, the distance measure is another point to ponder upon. There are several well-known distance measures (Euclidean, Chebyshev, Mahalanobis etc.) which you can use. Again, it depends upon prior-knowledge of your data and your ultimate task. These literature have information on Inter and Intra-cluster distances as well.
As a start, you can implement the K-Means clustering algorithm [3]. This is a well-known centroid-based clustering technique. You may use the Euclidean distance at first. The algorithm tries to minimize the intra-cluster variance (squared-Euclidean distance). Sometimes, the simplest of methods work well.
As far as the further implementation is concerned, almost all of the well-known software tools have cluster analysis packages. If you are at an university, you could use MATLAB [4] or prefer an open-source platform, you could try Python [5].
Good luck with your research!
Best Regards,
Rijul Soans
References:
[1] Everitt et al., "Cluster Analysis", Wiley Publishers, 2011
[2] Fukunaga eta al., "Introduction to Statistical Pattern Recognition", Academic Press, 2012
[3] Duda et al., "Pattern Classification", Wiley Publishers, 2012
maybe you are looking for measures as "silhouette" (Rousseeuw ,1986), providing insight of distances intra- and inter-cluster. I attached the wiki link where the silhouette is explained. Most of the software include libraries and toolboxes with this measure already coded. In addition, I also enclosed a couple of papers where are handled different issues with intra- and inter-cluster distances (with mixed data).