# Alignment on Reference Database **URL:** https://forum.qiime2.org/t/alignment-on-reference-database/10084 **Category:** User Support **Created:** [June 4, 2019, 12:04pm UTC](https://forum.qiime2.org/t/alignment-on-reference-database/10084 "2019-06-04T12:04:35Z") **Posts on this page:** 1 **Showing post:** 3
### Author: ![TurboQiimer](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/46a35a/32.png) [@TurboQiimer](https://forum.qiime2.org/u/TurboQiimer) #### Post date: [June 5, 2019, 10:08am UTC](https://forum.qiime2.org/t/alignment-on-reference-database/10084/3 "2019-06-05T10:08:54Z")
Let me give you an example. I was reading a paper written '_Sequences shorter than 300 nucleotides orlonger than 600 nucleotides were also discarded. The unique se-quences were then aligned in mothur by default setting with referring to the pre-aligned mcr Asequences provided by the Fun-gene Pipeline database_'. I do not need to draw a phylogeny tree. I want only align my sequences with a reference sequences. I found this message in Qiime2 forum: > [@Q2-alignment: reference based alignment using SINA](https://forum.qiime2.org/t/q2-alignment-reference-based-alignment-using-sina/6220): > > construction This is a draft Community Tutorial. construction The command qiime alignment sina may not yet be available in your installation of Qiime2 Comments and suggestions would be greatly appreciateed Aligning sequences to match a reference alignment Background Traditional, de novo methods mututally align a set of unaligned sequences to create a multiple sequence alignment (MSA) from scratch. Re-running these methods with additional sequences will create MSAs with varying numbers of… I am looking for a plugin/action/ method or tool in Qiime2 to align my sequences (query) with reference sequences. By the way, there is an alignemt option in Qiime2, Maff, but its function is de-novo. it does not align the query on the reference sequences. > **[mafft: De novo multiple sequence alignment with MAFFT — QIIME 2 2019.4.0...](https://docs.qiime2.org/2019.4/plugins/available/alignment/mafft/)** Now, can you help me with this details I gave to you? --- _[View the full topic](https://forum.qiime2.org/t/alignment-on-reference-database/10084)._