BEAST X issue with standard data / covarion model

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Horngyeh Jin

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Aug 15, 2025, 2:10:40 PMAug 15
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Hello everyone!
i'm using BEAST X and working on a pure morphological data input (standard datatype). I tried to do covarion analysis and set Sites > Substitution Model to "Covarion model" in Beauti, but then it keeps showing that "Parameter with name, bcov.alpha, is unknown", as in the following figure.
Do you have any idea of what's going on here?edb94274-2a88-48d4-af18-567cec136b58.png


and I have another problem. after importing a pure morphological data, if i keep Site > Base frequencies as "Estimated", it warns that "Parameters with name, frequencies, is unknown". if i choose "Empirical" here, the warning disappears.
What could have caused this issue?
219d3827-0095-4a21-9cbe-be096df12e0d.png

Horngyeh Jin

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Aug 22, 2025, 11:21:21 PMAug 22
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#NEXUS

Begin data;
dimensions ntax=3 nchar=11;
FORMAT DATATYPE = STANDARD INTERLEAVE GAP = - MISSING = ? SYMBOLS = "01";

MATRIX
Ax 01001101110
Bx 11001110110
Cx 10110?11001
;
end;



An example nexus file that could cause these errors is as above
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