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merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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Missing hmm databases #546

Closed ghost closed 7 years ago

ghost commented 7 years ago

Hi

I just installed the latest version of anvio to try out the single copy gene analyses and there's only two hmms: Campbell and Rinke. Alneberg and Creevey ones are not in the repo, is there a way i can get them as well.

Thank you.

meren commented 7 years ago

Hi,

We scaled down to those two have the appropriate noise filtering scores. They are here in the codebase:

https://github.com/merenlab/anvio/tree/master/anvio/data/hmm

It seems the last version we had them was v2.0.2:

https://github.com/merenlab/anvio/tree/v2.0.2/anvio/data/hmm

You can download these directories and use them with -H parameter in anvi-run-hmms after a bit of fixing (they need to look like the new ones in the latest repo, which includes an extra file).