I have just discovered Cluto as a way of clustering data which can be presented as a matrix. The standard format is as follows:
a p1 p2 p3 b p1 p2 p3 c p1 p2 p3
where each row is an entry and each column corresponds to a parameter.
I would like to compare and cluster protein sequences, including the sequence identity between each pair and I have a need to create, rather than a 2d matrix as above, a 3 dimensional matrix e.g., element (a P1) as an object with multiple parameters.
I cannot seem to find a way of doing this and I was wondering whether such a thing is possible? Is the only option to transform the data in some way to fit a 2d matrix?