Answers.Body: <p>Distance- and ML-based algorithms using reversible models can't find the root of trees. A classical method to root a tree is to use an outgroup (not outlier), which is a species/sequence <em>known</em> to directly descend from the root of the tree. In your case, it is relatively easy: add a chicken or fish ortholog to your dataset and put the root on the chicken/fish branch.</p>
  
  <p>Outgroup works well for single-copy genes used in species tree construction (e.g. ADH). However, it doesn't always work. The culprit is the "known" part. Say a gene has two copies A and B in vertebrates. Copy A was lost in rodent and copy B lost in primate. If you choose a chicken A gene as the outgroup, the correct tree should be ((primary-A,chicken-A),rodent-B). Without knowing the true history, you may forcefully put the root at the chicken-A branch and build a wrong tree ((primate-A,rodent-B),chicken-A).</p>
  
  <p>There are a few other tree rooting methods. An easy approach is to put the root at the longest branch in the tree, assuming the presence of molecular clock. When the species tree is known, you can root a gene tree by minimizing the number gene duplication/loss events in the history. I generally prefer the latter approach when the relevant information is available.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-11-29T01:51:40.557Z
Answers.Text: How to differentiate between outgroup and outlier? Thank you very much :) 
  @user172818
Answers.UserDisplayName: Zheng Keong Ng
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Answers.CreationDate: 2018-11-29T04:04:20.173Z
Answers.Text: @ZhengKeongNg In phylogenetics, "outlier" is not clearly defined. Avoid that word.
Answers.UserDisplayName: user172818
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Answers.CreationDate: 2018-11-29T00:43:49.130Z
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Answers.LastEditDate: 2018-11-29T13:02:07.610Z
Answers.UserDisplayName: user172818
Answers.Body: <p>you may use the OD-seq algorithm to filter outliers in a multiple alignment.
  <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0702-1" rel="nofollow noreferrer">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0702-1</a></p>
  
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Body: <p><a href="https://i.sstatic.net/g2fvb.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/g2fvb.png" alt="enter image description here"></a></p>
  
  <p>I an confused with the term 'outlier' and 'outgroup' in phylogeny. Could someone please explain with the example phylogenetic tree above which is the correct term? Thank you very much !!!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-30T14:43:34.193Z
Comments.Text: Welcome to the group.  Can you explain your question more.  What do you need explained about the tree?
Comments.UserDisplayName: Bioathlete
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-28T21:01:01.887Z
Comments.Text: An "outlier" is a term used in general statistics to infer that a minority of the data set deviates substantially from the majority. An example would be the number of radical substitutions present in a house-keeping gene. An outgroup is described below and singularly refers to phylogeny.
Comments.UserDisplayName: M__
Tags: <phylogenetics><phylogeny>
Title: What is outliers and how to determine outliers in the following phylogenetic tree?
ThreadText: # What is outliers and how to determine outliers in the following phylogenetic tree?
  
  (Asked by: username_0 on 2018-11-29)
  
  [![enter image description here](https://i.sstatic.net/g2fvb.png)](https://i.sstatic.net/g2fvb.png)
  
  I an confused with the term 'outlier' and 'outgroup' in phylogeny. Could someone please explain with the example phylogenetic tree above which is the correct term? Thank you very much !!!
  
  **Tags:** phylogenetics, phylogeny
  
  > **Comments:**
  > **username_1**: Welcome to the group.  Can you explain your question more.  What do you need explained about the tree?  
  > **username_2**: An "outlier" is a term used in general statistics to infer that a minority of the data set deviates substantially from the majority. An example would be the number of radical substitutions present in a house-keeping gene. An outgroup is described below and singularly refers to phylogeny.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2018-11-29. Score: 3 | Accepted answer
  
  Distance- and ML-based algorithms using reversible models can't find the root of trees. A classical method to root a tree is to use an outgroup (not outlier), which is a species/sequence *known* to directly descend from the root of the tree. In your case, it is relatively easy: add a chicken or fish ortholog to your dataset and put the root on the chicken/fish branch.
  
  Outgroup works well for single-copy genes used in species tree construction (e.g. ADH). However, it doesn't always work. The culprit is the "known" part. Say a gene has two copies A and B in vertebrates. Copy A was lost in rodent and copy B lost in primate. If you choose a chicken A gene as the outgroup, the correct tree should be ((primary-A,chicken-A),rodent-B). Without knowing the true history, you may forcefully put the root at the chicken-A branch and build a wrong tree ((primate-A,rodent-B),chicken-A).
  
  There are a few other tree rooting methods. An easy approach is to put the root at the longest branch in the tree, assuming the presence of molecular clock. When the species tree is known, you can root a gene tree by minimizing the number gene duplication/loss events in the history. I generally prefer the latter approach when the relevant information is available.
  
  > **Comments:**
  > **username_0**: How to differentiate between outgroup and outlier? Thank you very much :)  @username_3  
  > **username_3**: @username_0 In phylogenetics, "outlier" is not clearly defined. Avoid that word.  
  
  ---
  
  ### Answer by username_4 on 2020-05-07. Score: 0
  
  you may use the OD-seq algorithm to filter outliers in a multiple alignment.
  <https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0702-1>
  
  
  ---
  
  