MAKER beta not inferring gene models from protein evidence

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MAKER beta not inferring gene models from protein evidence

Timo Metz
Hey guys,

I have installed Maker v3 beta in order to use the built-in Evidence-Modeler which is not part of v2.31. Now I could see that, even if using the same evidence, the BUSCO completeness of the transcriptome drops when using the v3 beta compared to the v2.31. I could identify the reason leading to this was that MAKER v3 now does not infer gene models from Protein evidence if there is no additional support from RNA-seq/ests. In v2.31 it did, on the contrary. Is there any option in v3 beta to also get gene models only from protein evidence or is this something that v3 beta is not able to do anymore?

best
Timo

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