Is there a way to generate HMM-logos for the outputs of HMMER3? All tools seem to be limited to HMMER2, so neither LogoMat-M nor HMMeditor are working with my .hmm files.
Are there any recommendations how I could easily visualize such files to check the underlying model?
I don't know of tools for directly visualising HMMs in HMMER2 format. However, you can use hmmconvert to convert the HMMER3 files back to HMMER2 format.
Somehow I missed this option in the docu. I converted the files and everything works fine!
correct answer, but no upvote? :)
+1 for a clever but simple solution.