Invalid Fasta Files After Pargene

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Andrew

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Feb 10, 2022, 9:24:53 AMFeb 10
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Dear Benoit, 

I have been using generax after an inferring single gene trees using pargenes, and preparing my families file with the script supplied.

I noticed that my around 3318 of my families were classed as invalid. 

I checked the pargenes output for those families and it looked ok. 

But focusing on one example, I noticed that pargenes had selected model LG+I, but the families file was listing the model as LG+IU.

Sure enough, every failed family was listed as a model with "+IU" in the families file. 

Possibly just a bug in the script for preparing the families file in pargenes, but thought it might be useful for people to know. 

Thanks,
Andrew

Benoit Morel

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Feb 11, 2022, 3:03:29 AMFeb 11
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Dear Andrew,

Thanks for your message. Could you send me a subset of the alignments, such that I can reproduce and fix this?

Many thanks,
Benoit

Andrew

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Feb 18, 2022, 11:17:34 AMFeb 18
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Dear Benoit, 

So sorry I missed this response.

I will check through the files on Monday and pull out some of the alignments that had the issue.

I'd imagine it is just a problem with the families file python script supplied with pargenes/generax (I forgot which sorry!) 

Thanks,
Andrew

Andrew

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Feb 18, 2022, 11:18:29 AMFeb 18
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I should say, changing everything from LG+IU to LG+I resolved the problem for me and the families were no longer seen as invalid.
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