# Using Silva v119 in align.seqs and classify.seqs

**URL:** <https://forum.mothur.org/t/using-silva-v119-in-align-seqs-and-classify-seqs/1987>\
**Category:** Commands in mothur\
**Created:** [August 22, 2014, 7:39pm UTC](https://forum.mothur.org/t/using-silva-v119-in-align-seqs-and-classify-seqs/1987 "2014-08-22T19:39:12Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![hanshew](https://avatars.discourse-cdn.com/v4/letter/h/6bbea6/32.png) [@hanshew](https://forum.mothur.org/u/hanshew)\
**Post date:** [August 22, 2014, 7:39pm UTC](https://forum.mothur.org/t/using-silva-v119-in-align-seqs-and-classify-seqs/1987/1 "2014-08-22T19:39:12Z")

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I see the new Silva database that is now available on the wiki. I have read the ‘readme’ file. But I’m still confused.  
Normally I run align.seqs as such:  
align.seqs(fasta=Pigs4to6.shhh.trim.unique.fasta, reference=silva.all.Dec2012.fasta, flip=t)  
Where silva.all.Dec2012.fasta is the merged file for the last release (Dec2012 simply because that was the month I merged files).

Can silva.nr\_v119.align now be used as the alignment file as reference=silva.nr\_v119.align?

And then, how does this all combine with a nogap file when I go to run classify.seqs? Previously I had used:  
template=nogap.all.Dec2012.fasta, taxonomy=silva.all.silva.Dec2012.tax  
I think I understand that I’d use silva.nr\_v119.tax here, but what about the template file?

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:** [August 22, 2014, 9:05pm UTC](https://forum.mothur.org/t/using-silva-v119-in-align-seqs-and-classify-seqs/1987/2 "2014-08-22T21:05:05Z")

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> Can silva.nr\_v119.align now be used as the alignment file as reference=silva.nr\_v119.align?

Yes!

> And then, how does this all combine with a nogap file when I go to run classify.seqs? Previously I had used:  
> template=nogap.all.Dec2012.fasta, taxonomy=silva.all.silva.Dec2012.tax  
> I think I understand that I’d use silva.nr\_v119.tax here, but what about the template file?

So actually all the nogap stuff was unnecessary. mothur automatically removes the gaps from the reference/template file for you. So the fasta and tax files are all you need.

Pat

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**Author:** ![hanshew](https://avatars.discourse-cdn.com/v4/letter/h/6bbea6/32.png) [@hanshew](https://forum.mothur.org/u/hanshew)\
**Post date:** [August 25, 2014, 1:35pm UTC](https://forum.mothur.org/t/using-silva-v119-in-align-seqs-and-classify-seqs/1987/3 "2014-08-25T13:35:34Z")

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Thanks for you help!