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I have to work on multiple documents, some of which are under my control and I want to use Biblatex with Biber, others which require to use Bibtex.

I use Texmaker on Linux. I find it very annoying that there is only one global preferences for the bibliography backend (Options > Configure Texmaker > Bib(la)tex).

Is there a way to quickly switch between Biber and Bibtex depending on the document I am editing. That is, without having to edit the preferences all the time?

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You can define user macros. – Johannes_B Mar 13 '14 at 11:52
related: tex.stackexchange.com/questions/153359/… – Jubobs Mar 13 '14 at 11:56
You could also use arara. tex.stackexchange.com/questions/107989/… – Torbjørn T. Mar 13 '14 at 12:35

Thanks @johannes-b. So I can use User > User Commands. If you want to use the Wizard to assemble existing commands, one can abuse a predefined extry such as "Asymptote" (which I have never used) to run actually biber %, and leave Bib(la)tex for bibtex %.aux.

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Be warned in future you or someone may need Asymptote and it may create problems,don't configure asymptote entry with biber. I suggest you use Biber as User Commands in Texmaker see Making only biber as user command and leave Bib(la)tex for bibtex %.aux – texenthusiast Mar 13 '14 at 15:54

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