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I installed genometools with anaconda conda install -c bioconda genometools. Something is installed though apparently no binary called gt. If I type in gt Ubuntu suggests to install genometools via apt. What is the difference between both versions? Why is there no gt binary in the anaconda package?

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These appear to be two separate collections of tools. The conda version is a collection of python scripts whereas the apt version is based on a C library. So, as you might expect, the python version does not have a gt binary.

They also have separate GitHub accounts conda genometools vs apt genometools.

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