# Output all amino acids per CDS using Nextclade

**URL:** <https://nextstrain.discourse.group/t/output-all-amino-acids-per-cds-using-nextclade/1889>\
**Category:** General\
**Created:** [May 6, 2025, 7:32am UTC](https://nextstrain.discourse.group/t/output-all-amino-acids-per-cds-using-nextclade/1889 "2025-05-06T07:32:14Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![jonr](https://avatars.discourse-cdn.com/v4/letter/j/6f9a4e/32.png) [@jonr](https://nextstrain.discourse.group/u/jonr)\
**Post date:** [May 6, 2025, 7:32am UTC](https://nextstrain.discourse.group/t/output-all-amino-acids-per-cds-using-nextclade/1889/1 "2025-05-06T07:32:14Z")

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Hi,  
For Hepatitis C Virus some of the wildtype aa residues give resistance to certain drugs. I am therefore interested in making a list of all the residues at all positions of the CDS in the gff3 file, not only the differences to the reference. Is there an easy way to achieve this using Nextclade and some post-processing? I can probably make it work using the aligned sequence from Nextclade and the gff3-file, but maybe you already have a good suggestion?

Thanks, Jon

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**Author:** ![rneher](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/rneher/32/20_2.png) [@rneher](https://nextstrain.discourse.group/u/rneher)\
**Post date:** [May 7, 2025, 6:38am UTC](https://nextstrain.discourse.group/t/output-all-amino-acids-per-cds-using-nextclade/1889/2 "2025-05-07T06:38:41Z")

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Do I understand you correctly that a list of all residues at all positions would essentially amount to the full translation coding sequences? These would already be available as output. You can get them in the web application by downloading the `nextclade.peptides.fasta.zip` or using the CLI either by specifying a directory via `--output-all` or a specific path to where nextclade should put the translations.  
best,  
richard

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**Author:** ![jonr](https://avatars.discourse-cdn.com/v4/letter/j/6f9a4e/32.png) [@jonr](https://nextstrain.discourse.group/u/jonr)\
**Post date:** [May 7, 2025, 7:04am UTC](https://nextstrain.discourse.group/t/output-all-amino-acids-per-cds-using-nextclade/1889/3 "2025-05-07T07:04:33Z")

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Yes, you’re right I’m using the CLI, but hadn’t noticed that it’s possible to output the translated peptides… This is exactly what I need! Thanks! 🙂