# representative sequence and consensus sequence

**URL:** <https://forum.mothur.org/t/representative-sequence-and-consensus-sequence/1149>\
**Category:** Theory behind mothur\
**Created:** [December 7, 2012, 7:55am UTC](https://forum.mothur.org/t/representative-sequence-and-consensus-sequence/1149 "2012-12-07T07:55:30Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Jina\_OH](https://avatars.discourse-cdn.com/v4/letter/j/d9b06d/32.png) [@Jina\_OH](https://forum.mothur.org/u/Jina_OH)\
**Post date:** [December 7, 2012, 7:55am UTC](https://forum.mothur.org/t/representative-sequence-and-consensus-sequence/1149/1 "2012-12-07T07:55:30Z")

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I have a basic question.

What differences are there between the representative sequence and the consensus sequence of same OTU number?

If I construct the NJtree from the sequences, which sequences should I choose?

Thank you for answering, in advance^^

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**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\
**Post date:** [December 7, 2012, 3:19pm UTC](https://forum.mothur.org/t/representative-sequence-and-consensus-sequence/1149/2 "2012-12-07T15:19:12Z")

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The consensus sequence is not a real sequence - it’s the consensus of all the sequences in the OTU. The representative sequence is the sequence that is the shortest distance to all of the other sequences. I would foresee using the representative sequence as you describe and perhaps the consensus sequence for things like primer/probe design