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Title: Fix README: use correct conda command for environment.yml

Description: The current build instructions in the README suggest:

conda create --name fastMSA --file environment.yml -c pytorch -c conda-forge -c bioconda

This fails with the provided environment.yml because:

  • conda create --file expects a spec file, a plain text list of packages and versions, not a YAML environment definition.
  • The provided file is a full environment file with name:, channels:, and dependencies: keys.
  • When run as written, the command either fails to parse or ignores YAML structure.

Proposed change: Use:

conda env create -f environment.yml

This correctly parses the YAML, uses the embedded environment name (fastMSA), and respects the channels already defined in the file (pytorch, bioconda, conda-forge, defaults).

References:

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