PCPipe is a protein-clustering tool. The input is a set of ORFs and a FASTA file with already clustered ORFs. The process entails:Use cd-hit-2d to compare the input peptides to previously clustered proteinsThe result is a file with input proteins that clustered to existing clusters and those that did notUse the unclustered peptides and self-cluster them via cd-hitTake a representative sequence from each novel cluster, and use "blastp" to compare to SIMAP.Use the resulting SIMAP "feature_id" to look up the SIMAP features, merging the query results with the protein ID into a tab-delimited annotations fileProvide the user with two cluster files and the annotations for the new clusters based on the representative sequenceCode is freely available at Github.