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RAxML works with unrooted trees; however, the MLTreeMap pipeline reports all results in the context of rooted trees, for convenience (the re-rooting is hardcoded for each reference tree).
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These are hardcoded for English, so if using a different language, this should be set to false.
Note: The link name to be specified in the result template is hardcoded right now but this may change in a future version.
In practice, for each language element is defined a class and the referential checking is hardcoded on it.
The 'mskfile' input is now applied to point-source ARFs (previously, the mkarf 'mskfile' value was hardcoded as "NONE" as in psextract).
Nightingale stressed that a lot of the earlier design was hardcoded, and in order to make the customization features work, the team had to rewrite large parts of the interface to make it more flexible.
In the current implementation of the Vendor Modules, this information is either hardcoded in the corresponding module, or provided as configuration files which are read by the Vendor Modules.
Eventually the solutions to these straightforward challenges will be essentially hardcoded and built directly into the MR scanner.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com