# Remove.lineage

**URL:** <https://forum.mothur.org/t/remove-lineage/2302>\
**Category:** Commands in mothur\
**Created:** [March 16, 2015, 3:42pm UTC](https://forum.mothur.org/t/remove-lineage/2302 "2015-03-16T15:42:58Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Rich](https://avatars.discourse-cdn.com/v4/letter/r/35a633/32.png) [@Rich](https://forum.mothur.org/u/Rich)\
**Post date:** [March 16, 2015, 3:42pm UTC](https://forum.mothur.org/t/remove-lineage/2302/1 "2015-03-16T15:42:58Z")

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Dear mothur,

I would like to remove some specific groups from my taxonomy so I am using remove.lineage command.  
My question is if i am adding taxon name of lowest level will it remove its other levels such as Phylum/Class/order/family as well?

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**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [March 17, 2015, 2:48pm UTC](https://forum.mothur.org/t/remove-lineage/2302/2 "2015-03-17T14:48:37Z")

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Mothur will remove any sequence that matches to that level. Here’s an example:

AY457915 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospira(100);unclassified;unclassified;unclassified;  
AY457914 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospira(83);unclassified;unclassified;unclassified;  
AY457913 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(100);unclassified;unclassified;unclassified;  
AY457912 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospira(79);unclassified;unclassified;unclassified;  
AY457911 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);unclassified;unclassified;unclassified;

  
  
remove.lineage(taxonomy=abrecovery.silva.wang.taxonomy, taxon='Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Lachnospira;')

would produce:

AY457913 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(100);unclassified;unclassified;unclassified;  
AY457911 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);unclassified;unclassified;unclassified;

  
AY457915, AY457914 and AY457912 are removed because they belong to Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Lachnospira;.  
remove.lineage(taxonomy=abrecovery.silva.wang.taxonomy, taxon='Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;')

would produce:

AY457911 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);unclassified;unclassified;unclassified;

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<div class="post-metadata">

**Author:** ![Rich](https://avatars.discourse-cdn.com/v4/letter/r/35a633/32.png) [@Rich](https://forum.mothur.org/u/Rich)\
**Post date:** [March 18, 2015, 10:20am UTC](https://forum.mothur.org/t/remove-lineage/2302/3 "2015-03-18T10:20:52Z")

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Thank you so much for providing the solution.  
But i am not able to remove lineage together with - separation. When i am proving each taxon individually then its working but not with - (dash) separation.  
Its just removing the first one and not after that. I wonder if i have done some mistake. example below

mothur “#remove.lineage(fasta=file.fasta, name=file.names, group=file.groups, taxonomy=file.taxonomy,taxon=‘Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;Halomonadaceae;Halomonas;’- ‘Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Shewanellaceae;Shewanella;’-‘Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Micrococcaceae;Micrococcus;’)”

Thanks again!!!

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<div class="post-metadata">

**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [March 18, 2015, 2:16pm UTC](https://forum.mothur.org/t/remove-lineage/2302/4 "2015-03-18T14:16:35Z")

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It’s the ’ characters. Try this:

mothur “#remove.lineage(fasta=file.fasta, name=file.names, group=file.groups, taxonomy=file.taxonomy,taxon=‘Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;Halomonadaceae;Halomonas;-Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Shewanellaceae;Shewanella;-Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Micrococcaceae;Micrococcus;’)”

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<div class="post-metadata">

**Author:** ![Rich](https://avatars.discourse-cdn.com/v4/letter/r/35a633/32.png) [@Rich](https://forum.mothur.org/u/Rich)\
**Post date:** [March 20, 2015, 1:00pm UTC](https://forum.mothur.org/t/remove-lineage/2302/5 "2015-03-20T13:00:22Z")

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It worked thanks alot