BEAUTi cannot read .nex files

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Yuto Ozaki

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Jul 22, 2021, 12:50:04 AM7/22/21

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Hi all,

I have trouble with reading .nex files with BEAUTi. I would appreciate any advice!

I updated my BEAST to v2.6.5 (Windows), but then seemingly BEAUTi becomes not able to read .nex files properly. It gives an error message "Content is now allowed in prolog" when loading a .nex file, even the sample files contained in the examples folder. It looks like BEAUTi tries to read the .nex file as XML and interpret somewhere of the file as XML prolog. So, I decided to use a previous version (V2.6.3 Windows with JRE) and downloaded it from a release page (https://github.com/CompEvol/beast2/releases). However, I encountered another issue that BEAST seemingly automatically updates when launching the BEAUTi app. Even if I downloaded V2.6.3, the package manager of BEAUTi shows that V2.6.5 is installed, and indeed BEAST app shows the current version as V2.6.5, although the VERSION_HISTORY.txt says the version is V2.6.3. I cannot still edit .nex files with BEAUTi included in the v2.6.3 download content.

I also tried with a different computer. In the Mac version, I downloaded v2.6.4 w/ JRE, but in this case, BEAUTi does not allow choose .nex files from a file chooser dialog (but it is possible to choose XML files).

Is there anyone in a similar situation? I would like to create BEAST XML files via BEAUTi using .nex files, but the current situation does not allow that.

Yuto Ozaki

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Aug 9, 2021, 10:08:19 PM8/9/21

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Hi, I found there was a misunderstanding about the usage of BEAUTi. Issue solved.