# How to align a ITS dataset for more than 3000 sequences?

**URL:** <https://forum.mothur.org/t/how-to-align-a-its-dataset-for-more-than-3000-sequences/21418>\
**Category:** Uncategorized\
**Created:** [May 23, 2022, 9:33am UTC](https://forum.mothur.org/t/how-to-align-a-its-dataset-for-more-than-3000-sequences/21418 "2022-05-23T09:33:02Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![JPL](https://avatars.discourse-cdn.com/v4/letter/j/a9adbd/32.png) [@JPL](https://forum.mothur.org/u/JPL)\
**Post date:** [May 23, 2022, 9:33am UTC](https://forum.mothur.org/t/how-to-align-a-its-dataset-for-more-than-3000-sequences/21418/1 "2022-05-23T09:33:02Z")

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I’d like to analyse a fungal family. I download more than 3000 ITS sequences from GenBank.  
I tried to align them by mafft but performed not well.  
Could anyone tell me how to obtain a better alignment by mothur?  
Thank you very much.

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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:** [May 25, 2022, 1:15pm UTC](https://forum.mothur.org/t/how-to-align-a-its-dataset-for-more-than-3000-sequences/21418/2 "2022-05-25T13:15:37Z")

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Hi,

ITS sequences are not homologous to each other so generating a multiple sequence alignment from them really doesn’t work. I’d suggest using mothur’s `pre.cluster` instead.

Pat