Suitable for no model organisms? about compare_genomes HOT 3 OPEN

Yes, that should still be possible, but you may need to do the annotations of all the genomes included if the resources are scant. And Paramecium is one of the species with a PantherHMM database. You can have a look at the list for the most closely related species you may want to use.

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Thank you for getting back to me so quickly. I am currently working with green Tetrahymena, which we have sequenced and annotated. My plan is to compare it with all of the other reported full genome sequences of Tetrahymena species from the TGD database. I am wondering if it is necessary to use the pather_HMM database for this pipeline. My ultimate goal is to study gene expansion/contraction and analyze Ka/Ks.

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No worries. That's also possible if you want to classify the orthogroups (output of OrthoFinder) yourself. You may work on the output of OrthoFinder directly if you wish and perform CAFE expansion/contraction analyses on them with or without classifying the orthogroups (i.e. attaching biological function or most likely gene families to each orthogroup).

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