Tree simulation also requires a mutability model, but the idea would be to force any user to bring their own appropriate model when one is needed.
We now expect comma-separated, unquoted mutability and substitution files, where before we expected tab-separated, quoted files. This PR still allows loading files in the old format, but only the new format is mentioned in the docs, so as soon as this PR is merged, the docs will tell lies about the most recent gctree release, until this PR makes it into a new release.
In order to avoid misleading users about new experimental ranking criteria (mutability and isotype parsimony), this PR does these things:
We now expect comma-separated, unquoted mutability and substitution files, where before we expected tab-separated, quoted files. This PR still allows loading files in the old format, but only the new format is mentioned in the docs, so as soon as this PR is merged, the docs will tell lies about the most recent gctree release, until this PR makes it into a new release.