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As it may be difficult to determine which is the correct choice of program to leverage, we offer the following usage/troubleshooting flowchart helpfully generated by collaborators at the Center for Computational Medicine (CCB), with whom we held a town hall regarding Alphafold and ColabFold. More information about the town hall can be found at the CCB website.
For users interested in running large volumes of predictions with LocalColabFold, we strongly recommend getting familiar with the local mmseqs2 alignment procedure (https://harvardmed.atlassian.net/wiki/spaces/O2/pages/2180546561/Using+Local+ColabFold+on+O2#Generating-MSAs-Using-Local-MMseqs2 ). This is crucial to avoid getting bottlenecked or blacklisted by the remote server.
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Please contact rchelp@hms.harvard.edu for any questions or clarification.