# MAFFT input in open-reference OTU picking workflow

**URL:** https://forum.qiime2.org/t/mafft-input-in-open-reference-otu-picking-workflow/2082
**Category:** User Support
**Tags:** mafft
**Created:** [December 4, 2017, 5:09pm UTC](https://forum.qiime2.org/t/mafft-input-in-open-reference-otu-picking-workflow/2082 "2017-12-04T17:09:15Z")
**Posts on this page:** 4
**Page:** 1

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### Author: ![steff1088](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/s/c89c15/32.png) [@steff1088](https://forum.qiime2.org/u/steff1088)
#### Post date: [December 4, 2017, 5:09pm UTC](https://forum.qiime2.org/t/mafft-input-in-open-reference-otu-picking-workflow/2082/1 "2017-12-04T17:09:15Z")

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@Nicholas_Bokulich thanks a lot.

From my workflow up to the classification and plotting, what intermediate file would I use as input to MAFFT in order to work on getting a rooted tree?

-steffen

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### Author: ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [December 4, 2017, 5:31pm UTC](https://forum.qiime2.org/t/mafft-input-in-open-reference-otu-picking-workflow/2082/2 "2017-12-04T17:31:17Z")

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Thanks for asking, @steff1088! In general this would be the same exact sequences file that you use as input for taxonomy classification, e.g., could be as simple as the `rep-seqs.qza` output from `cluster-features-open-reference`. However, in your case (since you apply an abundance filter to the feature table and then remove these features from the sequences file) you could use the filtered sequences.

I hope that helps!

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### Author: ![steff1088](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/s/c89c15/32.png) [@steff1088](https://forum.qiime2.org/u/steff1088)
#### Post date: [December 4, 2017, 5:32pm UTC](https://forum.qiime2.org/t/mafft-input-in-open-reference-otu-picking-workflow/2082/3 "2017-12-04T17:32:27Z")

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Wonderful, thanks for this advice as well.

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### Author: ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)
#### Post date: [January 4, 2018, 11:32pm UTC](https://forum.qiime2.org/t/mafft-input-in-open-reference-otu-picking-workflow/2082/4 "2018-01-04T23:32:33Z")

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