# ARO id to antibiotics clusters

**URL:** <https://forum.biobakery.org/t/aro-id-to-antibiotics-clusters/628>\
**Category:** ShortBRED\
**Created:** [June 24, 2020, 2:09am UTC](https://forum.biobakery.org/t/aro-id-to-antibiotics-clusters/628 "2020-06-24T02:09:19Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Qiuyu\_Jing](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/qiuyu_jing/32/200_2.png) [@Qiuyu\_Jing](https://forum.biobakery.org/u/Qiuyu_Jing)\
**Post date:** [June 24, 2020, 2:09am UTC](https://forum.biobakery.org/t/aro-id-to-antibiotics-clusters/628/1 "2020-06-24T02:09:19Z")

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Hi,

May i know that how i can cluster the antibiotics families quantified from ShortBRED to larger antibiotics resistant group based on ARO id? like the heatmap in 2015-paper?

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**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\
**Post date:** [June 24, 2020, 3:25pm UTC](https://forum.biobakery.org/t/aro-id-to-antibiotics-clusters/628/2 "2020-06-24T15:25:49Z")

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Those families were a result of the initial clustering step in ShortBRED. Specifically, proteins of interest are clustered based on high identity and coverage using CD-HIT and then multiply aligned with MUSCLE. A single member of the cluster is chosen as a representative for naming purposes.

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**Author:** ![Qiuyu\_Jing](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/qiuyu_jing/32/200_2.png) [@Qiuyu\_Jing](https://forum.biobakery.org/u/Qiuyu_Jing)\
**Post date:** [June 25, 2020, 5:28pm UTC](https://forum.biobakery.org/t/aro-id-to-antibiotics-clusters/628/3 "2020-06-25T17:28:14Z")

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Thanks franzosa.  
Actually i encountered another problem when using shortbred\_identify.py. it shows there are some invalid id in my sequence file. I need to use utils/AdjustFastaHeadersForShortBRED.py. But i can not find this utils. When i call python utils/AdjustFastaHeadersForShortBRED.py, it says no such file.

I installed ShortBRED using conda. And also can not find this package under python’s site-package folders.