Answers.Body: <p>Your isolates are both robustly part of the NCBI lineage of 4, i.e. now making a lineage of 8 taxa and genetically very close to it, but slightly distinct.</p>
  <p>The robustness is given by the bootstrap values (100) and the genetic proximity is given by the genetic distances for each branch. What you want to do is look at the epidemiological information for your strains and those in Genbank, there should be some sort of recognised association, e.g. country, possibly locality, anything else?</p>
  <p>The association has epidemiological significance, thus it's not random, if that is your question. There will definitely something connecting this lineage of 8.</p>
  
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Answers.CreationDate: 2023-11-15T11:32:53.073Z
Answers.Text: Yes, they indeed are from same country. Thank you very much!!
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Body: <p>This might be something very trivial to ask, but I am new to this and was confused as in how to identify or differentiate between very closely related isolates from clonal isolate from the whole genome/core-genome phylogeny?</p>
  <p>For instace, I am drawing a core-genome phylogeny of Staphylococcus aureus genomes taken from NCBI as well as from my own sequenced ones. Now, my isolates have grouped with several isolates from NCBI (Bottom four greens with four red ones). I want to know, weather these isolates are actually closely related to NCBI ones or they are just those strains themselves?</p>
  <p><a href="https://i.sstatic.net/diGK7.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/diGK7.png" alt="enter image description here" /></a></p>
  <p>Thank you all in advance!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-10T10:41:18.850Z
Comments.Text: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.
Comments.UserDisplayName: Community
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Comments.CreationDate: 2023-11-10T10:56:51.407Z
Comments.Text: Please [edit] and tell us what you are doing, what kind of data you are working with etc.
Comments.UserDisplayName: terdon
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Comments.Text: Can you provide a tree that represents your data? If you do that I'll explain how to interpret it.
Comments.UserDisplayName: M__
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Comments.Text: Thank you very much for the reply! I have tried to add details to the best of my understanding!
Comments.UserDisplayName: prekij
Tags: <phylogeny><genomics>
Title: Confirming Identity of clone in Phylogeny
ThreadText: # Confirming Identity of clone in Phylogeny
  
  (Asked by: username_0 on 2023-11-10)
  
  This might be something very trivial to ask, but I am new to this and was confused as in how to identify or differentiate between very closely related isolates from clonal isolate from the whole genome/core-genome phylogeny?
  
  For instace, I am drawing a core-genome phylogeny of Staphylococcus aureus genomes taken from NCBI as well as from my own sequenced ones. Now, my isolates have grouped with several isolates from NCBI (Bottom four greens with four red ones). I want to know, weather these isolates are actually closely related to NCBI ones or they are just those strains themselves?
  
  [![enter image description here](https://i.sstatic.net/diGK7.png)](https://i.sstatic.net/diGK7.png)
  
  Thank you all in advance!
  
  **Tags:** phylogeny, genomics
  
  > **Comments:**
  > **username_1**: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.  
  > **username_2**: Please [edit] and tell us what you are doing, what kind of data you are working with etc.  
  > **username_3**: Can you provide a tree that represents your data? If you do that I'll explain how to interpret it.  
  > **username_0**: Thank you very much for the reply! I have tried to add details to the best of my understanding!  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2023-11-15. Score: 1 | Accepted answer
  
  Your isolates are both robustly part of the NCBI lineage of 4, i.e. now making a lineage of 8 taxa and genetically very close to it, but slightly distinct.
  
  The robustness is given by the bootstrap values (100) and the genetic proximity is given by the genetic distances for each branch. What you want to do is look at the epidemiological information for your strains and those in Genbank, there should be some sort of recognised association, e.g. country, possibly locality, anything else?
  
  The association has epidemiological significance, thus it's not random, if that is your question. There will definitely something connecting this lineage of 8.
  
  > **Comments:**
  > **username_0**: Yes, they indeed are from same country. Thank you very much!!  
  
  ---
  
  