Answers.Body: <p>When looking at genomic data for bacteria, taxa above the species level are operational taxonomic units (OTUs). OTUs are designated based on percent identity of the sequence (specifically the 16S rRNA gene sequences in most cases). The classification is usually based on rule of thumb, and some rough guidelines are:</p>
  
  <ul>
  <li>97% for Genus</li>
  <li>94% for Family</li>
  <li>88% for Order</li>
  </ul>
  
  <p>Using OTUs is common practice. I don't see much of an ideological difference using OTUs with synthetic data.</p>
  
  <p><em>Konstantinidis, K. T., &amp; Tiedje, J. M. (2005). Towards a Genome-Based Taxonomy for Prokaryotes. Journal of Bacteriology, 187(18), 6258–6264. <a href="http://doi.org/10.1128/JB.187.18.6258-6264.2005" rel="nofollow noreferrer">http://doi.org/10.1128/JB.187.18.6258-6264.2005</a></em></p>
  
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Answers.CreationDate: 2017-09-07T12:56:51.187Z
Answers.Text: OTUs are restricted to above the species level: they can be used for any group of closely related individuals. The use of OTU is meant to be agnostic as to actual group or relationship, underlining that the grouping was arrived at "operationally", i.e. methodologically. In any event, my feeling is that the context in which OTU is usually used is fairly distinct to a generic phylogenetic problem.
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Answers.UserDisplayName: Kohl Kinning
Answers.Body: <p>Phylogenies can be made with/of non-species groups. I think "taxon" is perfectly fine. You might also consider the use of the "leaf / leaves" or "terminal" if you want to emphasise the tip nature of the organisms. Even "sequence" would be fine.</p>
  
  <p>Ninja edit to my own suggestion: since you're making a phylogeny from sequences of unknown context or relationship (i.e. you can't say that they're sequences from a "species" or "OTU" or from anywhere), agnostic terms like "taxon" or "sequence" are more correct.</p>
  
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Answers.Text: 'Taxon' seems to be frequently used in the literature for simulated sequences. See [this](https://academic.oup.com/mbe/article/23/11/2090/1325821/Exploring-the-Relationship-between-Sequence) or [this](https://academic.oup.com/mbe/article/19/6/950/1094968/Accuracy-and-Power-of-Bayes-Prediction-of-Amino) for example
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Answers.UserDisplayName: agapow
Body: <p>For the purpose of testing phylogenetics software, we're using synthetic sequence data (i.e., it's computer generated, and there's no actual biological organism with that e.g. DNA sequence).  For real-world biological sequence data, we would say the sequence belongs to a "species" or "<a href="https://en.wikipedia.org/wiki/Taxon" rel="noreferrer">taxon</a>" (or "taxonomic group"), but this feels inaccurate since there is no actual species or taxon.</p>
  
  <p><strong>Question</strong>: Can we describe synthetic biological sequence data as belonging to a "species" or "taxon"?</p>
  
  <p>I'm wondering if this is standard practice, despite the synthetic nature of the data.</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-09-07T09:57:13.457Z
Comments.Text: How were the synthetic reads generated exactly?
Comments.UserDisplayName: Chris_Rands
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-09-07T10:57:51.860Z
Comments.Text: Using evolver, packaged with [PAML](http://abacus.gene.ucl.ac.uk/software/paml.html).
Comments.UserDisplayName: Rebecca J. Stones
Tags: <terminology><phylogenetics>
Title: Can we describe synthetic biological sequence data as belonging to a "species" or "taxon"?
ThreadText: # Can we describe synthetic biological sequence data as belonging to a "species" or "taxon"?
  
  (Asked by: username_0 on 2017-09-07)
  
  For the purpose of testing phylogenetics software, we're using synthetic sequence data (i.e., it's computer generated, and there's no actual biological organism with that e.g. DNA sequence). For real-world biological sequence data, we would say the sequence belongs to a "species" or "[taxon](https://en.wikipedia.org/wiki/Taxon)" (or "taxonomic group"), but this feels inaccurate since there is no actual species or taxon.
  
  **Question**: Can we describe synthetic biological sequence data as belonging to a "species" or "taxon"?
  
  I'm wondering if this is standard practice, despite the synthetic nature of the data.
  
  **Tags:** terminology, phylogenetics
  
  > **Comments:**
  > **username_1**: How were the synthetic reads generated exactly?  
  > **username_0**: Using evolver, packaged with [PAML](http://abacus.gene.ucl.ac.uk/software/paml.html).  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2017-09-07. Score: 6 | Accepted answer
  
  Phylogenies can be made with/of non-species groups. I think "taxon" is perfectly fine. You might also consider the use of the "leaf / leaves" or "terminal" if you want to emphasise the tip nature of the organisms. Even "sequence" would be fine.
  
  Ninja edit to my own suggestion: since you're making a phylogeny from sequences of unknown context or relationship (i.e. you can't say that they're sequences from a "species" or "OTU" or from anywhere), agnostic terms like "taxon" or "sequence" are more correct.
  
  > **Comments:**
  > **username_4**: 'Taxon' seems to be frequently used in the literature for simulated sequences. See [this](https://academic.oup.com/mbe/article/23/11/2090/1325821/Exploring-the-Relationship-between-Sequence) or [this](https://academic.oup.com/mbe/article/19/6/950/1094968/Accuracy-and-Power-of-Bayes-Prediction-of-Amino) for example  
  
  ---
  
  ### Answer by username_2 on 2017-09-07. Score: 2
  
  When looking at genomic data for bacteria, taxa above the species level are operational taxonomic units (OTUs). OTUs are designated based on percent identity of the sequence (specifically the 16S rRNA gene sequences in most cases). The classification is usually based on rule of thumb, and some rough guidelines are:
  
  * 97% for Genus
  * 94% for Family
  * 88% for Order
  
  Using OTUs is common practice. I don't see much of an ideological difference using OTUs with synthetic data.
  
  *Konstantinidis, K. T., & Tiedje, J. M. (2005). Towards a Genome-Based Taxonomy for Prokaryotes. Journal of Bacteriology, 187(18), 6258–6264. <http://doi.org/10.1128/JB.187.18.6258-6264.2005>*
  
  > **Comments:**
  > **username_3**: OTUs are restricted to above the species level: they can be used for any group of closely related individuals. The use of OTU is meant to be agnostic as to actual group or relationship, underlining that the grouping was arrived at "operationally", i.e. methodologically. In any event, my feeling is that the context in which OTU is usually used is fairly distinct to a generic phylogenetic problem.  
  
  ---
  
  