# alignment

**URL:** <https://forum.mothur.org/t/alignment/2870>\
**Category:** Commands in mothur\
**Created:** [May 27, 2016, 9:22am UTC](https://forum.mothur.org/t/alignment/2870 "2016-05-27T09:22:33Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Ari](https://avatars.discourse-cdn.com/v4/letter/a/5f8ce5/32.png) [@Ari](https://forum.mothur.org/u/Ari)\
**Post date:** [May 27, 2016, 9:22am UTC](https://forum.mothur.org/t/alignment/2870/1 "2016-05-27T09:22:33Z")

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Hey to all , we have a problem with the align.seqs command , we would to analyze function genes, and we try many different parameters , but mothur is inserting to many unnecessary gaps despite a correct reference alignment without gaps , How we can fix this problem, and wich parameters can we used for it ?

Thanks

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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 28, 2016, 10:56am UTC](https://forum.mothur.org/t/alignment/2870/2 "2016-05-28T10:56:37Z")

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Can you explain how you have a reference alignment that doesn’t have gaps?

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**Author:** ![Ari](https://avatars.discourse-cdn.com/v4/letter/a/5f8ce5/32.png) [@Ari](https://forum.mothur.org/u/Ari)\
**Post date:** [May 30, 2016, 7:49am UTC](https://forum.mothur.org/t/alignment/2870/3 "2016-05-30T07:49:29Z")

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The reference file just have gaps , but mothur insert new gaps in false postions instead of the alignment corectly of the reference alignment wich paramters do we have to change to avoid these problems.

Best Regards

Ari

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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 31, 2016, 1:04pm UTC](https://forum.mothur.org/t/alignment/2870/4 "2016-05-31T13:04:06Z")

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If you could send your reference file and an example sequence to mothur.bugs at [gmail.com](http://gmail.com) with the url for this thread we can take a look.

Pat