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Protein sequence clustering

I am using cd-hit to cluster a number of protein sequences. cd-hit picks any sequence as a centroid when there are a number of identical sequences with 100% identity in a cluster. I would like to include a number of pre-defined centroids for the clustering and I think cd-hit cannot do that whereas it was possible to provide a library file in uclust. Sequences are searched against this library file and new cluster seeds would be defined if the input sequences did not match the library sequences.

I was wondering if it is possible to this with cd-hit. cd-hit-2d can be used to search against a predefined database/library but doesn't quite work like following uclust solution. I am unable to find a usearch equivalent solution for the following command and would like to use a tool is not discontinued like uclust.

uclust --usersort --input input.fa --lib seeds.fa --uc uclust_output --id 0.90
cd-hit protein sequences clustering
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written by Sej Modha Sej Modha

Clarification: I would like to use a list of preferred representative sequences in cd-hit.

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written by Sej Modha Sej Modha

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