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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???

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???

clustering
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updated by Jan Kosinski Jan Kosinski • written by Sonali • Sonali

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

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written by Michael Dondrup Michael Dondrup

1 answer

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.

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written by Jan Kosinski Jan Kosinski

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

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written by Michael Dondrup Michael Dondrup

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