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thomas-bailly edited this page Sep 24, 2024
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Welcome to the CAESAR wiki!
CAESAR is a pipeline to (1) search candidates sequence, based on reference sequences or hmm pattern, (2) cluster them, (3) select candidates in each cluster and (4) build a phylogenetic tree.
The Usages page explains how to use each subcommand to setting up options and start the workflow at different steps.
The File Format page lists and explains the format of the outputs. Some of these outputs are required to start the workflow after the Search step (Blastp or Hmmsearch). The user must know how to format them properly.