# cutoff in classify.seqs

**URL:** <https://forum.mothur.org/t/cutoff-in-classify-seqs/1112>\
**Category:** Commands in mothur\
**Created:** [November 1, 2012, 8:01pm UTC](https://forum.mothur.org/t/cutoff-in-classify-seqs/1112 "2012-11-01T20:01:58Z")\
**Posts on this page:** 6\
**Page:** 1

<div class="post-metadata">

**Author:** ![newbie](https://avatars.discourse-cdn.com/v4/letter/n/dc4da7/32.png) [@newbie](https://forum.mothur.org/u/newbie)\
**Post date:** [November 1, 2012, 8:01pm UTC](https://forum.mothur.org/t/cutoff-in-classify-seqs/1112/1 "2012-11-01T20:01:58Z")

</div>

Hello Everyone,  
I am kind of confused, what does cutoff in classify.seqs() mean? Is it taking the SearchScore percentage from the align.report file. I provided 80,95,99 cutoff and then I used classify.ots() command to generate OTUs and everytime it is giving me same no. of OTUs.  
Also, I am using Silva db, I used silva bacteria, archaea and eukaryotes separately but to my surprise the archaea is generating more OTUs than bacteria and I am getting OTUs in eukaryotes also. How is that possible as I have only 16s sequences.

Thanks for the help!!!

---

<div class="post-metadata">

**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:** [November 2, 2012, 12:26pm UTC](https://forum.mothur.org/t/cutoff-in-classify-seqs/1112/2 "2012-11-02T12:26:39Z")

</div>

[http://www.mothur.org/wiki/Classify.seqs#cutoff](http://www.mothur.org/wiki/Classify.seqs#cutoff)

---

<div class="post-metadata">

**Author:** ![newbie](https://avatars.discourse-cdn.com/v4/letter/n/dc4da7/32.png) [@newbie](https://forum.mothur.org/u/newbie)\
**Post date:** [November 2, 2012, 6:47pm UTC](https://forum.mothur.org/t/cutoff-in-classify-seqs/1112/3 "2012-11-02T18:47:41Z")

</div>

> [@pschloss](#):
>
> [Redirecting…](http://www.mothur.org/wiki/Classify.seqs#cutoff)

Thanks Dr. Schloss,  
I read it before but didn’t get why I am getting same number of OTUs at different cutoffs. And also, why I am getting OTUS with eukaryotes when it is 16s. The align.report did show some matches for ex:  
1-1023 151 U94371.1 1734 kmer 7.64 needleman 150 151 1 2 2 0 0 0 100.00  
2-810 151 AJ243682.1 1758 kmer 6.25 needleman 1 14 1747 1758 14 0 2 1 57.14  
3-774 151 AF352087.1 2059 kmer 9.03 needleman 147 151 1 5 5 0 0 0 100.00  
4-772 151 L24747.1 1742 kmer 10.42 needleman 1 151 200 355 162 11 6 1 56.17  
5-572 151 U51005.1 1733 kmer 6.25 needleman 150 151 1 2 2 0 0 0 100.00

for the first one the SimBtwnQuery&Template is 100 but the search score is just 7.64. I am wondering if the commands somewhere we are removing theses bad matched and then generating OTUs. I got that the cutoff is bootstraping value but where is the step in which we are removing the bad alignments.

Sorry for all the basic question but I am not getting it.

Thanks!!!

---

<div class="post-metadata">

**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:** [November 2, 2012, 9:14pm UTC](https://forum.mothur.org/t/cutoff-in-classify-seqs/1112/4 "2012-11-02T21:14:37Z")

</div>

Well your questions are confusing too! 🙂 You are mixing classify.seqs and cluster or phylotype. I really don’t know what you’re trying to ask.

---

<div class="post-metadata">

**Author:** ![newbie](https://avatars.discourse-cdn.com/v4/letter/n/dc4da7/32.png) [@newbie](https://forum.mothur.org/u/newbie)\
**Post date:** [November 12, 2012, 7:49pm UTC](https://forum.mothur.org/t/cutoff-in-classify-seqs/1112/5 "2012-11-12T19:49:03Z")

</div>

> [@pschloss](#):
>
> Well your questions are confusing too! 🙂 You are mixing classify.seqs and cluster or phylotype. I really don’t know what you’re trying to ask.

Hi Dr. Schloss,  
I just want to know what does cut-off implies to in classify.seqs()

Thanks!!!

---

<div class="post-metadata">

**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:** [November 12, 2012, 11:17pm UTC](https://forum.mothur.org/t/cutoff-in-classify-seqs/1112/6 "2012-11-12T23:17:36Z")

</div>

It corresponds to the confidence threshold. If an assignment is below the threshold, classify.seqs reports the next assignment above the threshold.