generate_msa.py --start-query: unclear how to provide a query FASTA #65
Description
Hi EvoDiff maintainers — thank you for open-sourcing EvoDiff.
I’m trying to generate an MSA starting from a user-provided single query sequence (custom FASTA), but I can’t find an example or documentation showing how to pass an input query sequence to generate_msa.py.
The README mentions a --start-query mode (“starts with the query and generates the alignment”), but it’s unclear how the query sequence itself should be specified (e.g., via a FASTA file or command-line argument).
Could you clarify whether --start-query is currently intended to sample a query from the OpenFold validation data (rather than accept a user-provided sequence), unless the code is modified? If there is a recommended way to provide a custom query FASTA, I would appreciate guidance or an example. Thanks again.