Hi!! As I Have To Cluster Pdbs On The Basis Of Rmsd Matrix I Generated. Can Any One Suggest Me What Can Be The Suitable Way To Do That As The Phylip Is Not Accepting The Matrix As Such???

Question

[Sonali]

Hi!! As I have to cluster pdbs on the basis of RMSD matrix I generated. Can any one suggest me what can be the suitable way to do that as the Phylip is not accepting the matrix as such???

[Michael]

some hints, shorten your title, therefore provide an example and describe how you created a matrix.

Answer 1

[Jan Kosinski]

There are numerous programs to do clustering on existing distance matrix but you can try with MaxCluster It is designed for tertiary structures, it accepts an existing RMSD matrix in a special format (you will have to re-format yours).

BTW. the PHYLIP programs of course do accept distance matrices. The NEIGHBOR program could be suitable for your purposes. You must probably re-format yours.

[Michael]

helpful answer, given the level of information provided by the op +1