# Identifying Strain Names

**URL:** <https://forum.biobakery.org/t/identifying-strain-names/2493>\
**Category:** StrainPhlAn\
**Created:** [August 19, 2021, 7:00am UTC](https://forum.biobakery.org/t/identifying-strain-names/2493 "2021-08-19T07:00:17Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Dario](https://avatars.discourse-cdn.com/v4/letter/d/bc79bd/32.png) [@Dario](https://forum.biobakery.org/u/Dario)\
**Post date:** [August 19, 2021, 7:00am UTC](https://forum.biobakery.org/t/identifying-strain-names/2493/1 "2021-08-19T07:00:17Z")

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My aim is to identify well-known strains in my own samples. For example, in a recent journal article titled [RNA Landscape of the Emerging Cancer-associated Microbe _Fusobacterium nucleatum_](https://www.nature.com/articles/s41564-021-00927-7), the introduction contains

> … we generate high-resolution global RNA maps for five clinically relevant fusobacterial strains— _F. nucleatum_ subspecies _nucleatum_, _animalis_, _polymorphum_ and _vincentii_, as well as _F. periodonticum_

Can StrainPhlAn do that? I can’t find anything in its user guide that suggests I could identify Fusobacterium nucleatum subsp. nucleatum, for instance. Is StrainPhlAn only for calculating the number of SNPs to a species reference genome?

> **Step 2.** Obtain the sam files from these samples by mapping them against MetaPhlAn database  
> **Step 4.** Extract the markers of _Bacteroides\_caccae_ from MetaPhlAn database

Isn’t the database called ChocoPhlAn? MetaPhlAn is the name of a software.

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**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [August 23, 2021, 9:22am UTC](https://forum.biobakery.org/t/identifying-strain-names/2493/2 "2021-08-23T09:22:22Z")

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Hi @Dario  
Thanks for getting in touch. For identify well-known strains in your samples you first need to include them as `reference genomes` when calling StrainPhlAn (using the `-r / --references` parameter). Once StrainPhlAn generates the tree, you can check whether the strains you included are also present in your samples by checking their phylogenetic distance in the tree. Please, see this last post: [Strain Identity Cutoff](https://forum.biobakery.org/t/strain-identity-cutoff/1094)