# how to make custom reference sequence?

**URL:** <https://forum.mothur.org/t/how-to-make-custom-reference-sequence/1976>\
**Category:** Commands in mothur\
**Created:** [August 11, 2014, 9:03am UTC](https://forum.mothur.org/t/how-to-make-custom-reference-sequence/1976 "2014-08-11T09:03:57Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![xiaojay](https://avatars.discourse-cdn.com/v4/letter/x/3ab097/32.png) [@xiaojay](https://forum.mothur.org/u/xiaojay)\
**Post date:** [August 11, 2014, 9:03am UTC](https://forum.mothur.org/t/how-to-make-custom-reference-sequence/1976/1 "2014-08-11T09:03:57Z")

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hello

i want use align.seqs command to align some sequeces to my own set of reference sequences?

howerver, i got error “[ERROR]: template is not aligned, aborting.”

so my question is how to make custom reference sequence ?

thanks 🙂

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<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:** [August 13, 2014, 12:00pm UTC](https://forum.mothur.org/t/how-to-make-custom-reference-sequence/1976/2 "2014-08-13T12:00:36Z")

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The reference sequences must themselves be aligned to each other. You can pull sequences out of a reference database like we have for the SILVA and greengenes references. Alternatively, you can align protein coding sequences using something like clustal.

Pat