Body: <p>I am looking into different methods to test the long-branch attraction problem. In <a href="https://www.sciencedirect.com/science/article/pii/B9780444536327011084" rel="nofollow noreferrer">this chapter</a> they talk about the SAW method - excluding one and the other taxa from the dataset and see if they change their position within the tree. From the description of the method, I was not sure, if the bunch of sequences with excluded samples should be realigned, or if I should simply exclude the rows in the alignment.</p>
  <p>I tried to figure out it by looking at the <a href="https://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.1999.tb00391.x" rel="nofollow noreferrer">Siddall and Whiting 1995</a> paper, which was referred to as the original description of this method in the chapter mentioned above. The best I found is</p>
  <blockquote>
  <p>Using their alignment (<a href="http://biology.unm.edu/esloker/" rel="nofollow noreferrer">http://biology.unm.edu/esloker/</a>), when Polypodium is excluded, the most parsimonious tree groups the myxozoans as sister to the Bilateria (Fig. 1a).</p>
  </blockquote>
  <p>which makes me think that we should just exclude the taxa from the final alignment, but as there is still a space for interpretation, I thought I'll ask.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-09-06T14:58:36.020Z
Comments.Text: In my opinion, since the aim of the SAW test and other leave-one-out approaches like it is to minimise the variance associated with any factor other than the taxon sampling, you should leave the alignment as-is and simply exclude the row of the associated taxon.
Comments.UserDisplayName: NatWH
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-09-06T15:00:09.147Z
Comments.Text: Of course, things on long branches can often be annoyingly divergent and induce long internal INDELs and other weird alignment patterns. So I suspect it depends on exactly how much the homology statements in the alignment would change if you reinferred it dropping the taxon. Easiest way is just to try both (with realign, without realign) and compare.
Comments.UserDisplayName: NatWH
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-09-08T20:14:23.093Z
Comments.Text: That's already quite close to an answer, thanks @NatWH. (trying to subtly encourage you to write one)
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-09-10T00:10:10.650Z
Comments.Text: I agree more with @NatWH's second comment. the idea of the test is to exclude all sources of information from the branch. Especially if the concern is long branches, the clustering that is implicit in the multiple alignment are likely to become nontrivial sources of information. One suspects also that choice of aligner (e.g. structure of initial heuristic steps) is also likely to interact with this.
Comments.UserDisplayName: Maximilian Press
Tags: <phylogenetics><phylogeny>
Title: Does the alignment need to be redone when using SAW method to test long branch attraction?
ThreadText: # Does the alignment need to be redone when using SAW method to test long branch attraction?
  
  (Asked by: username_0 on 2021-09-06)
  
  I am looking into different methods to test the long-branch attraction problem. In [this chapter](https://www.sciencedirect.com/science/article/pii/B9780444536327011084) they talk about the SAW method - excluding one and the other taxa from the dataset and see if they change their position within the tree. From the description of the method, I was not sure, if the bunch of sequences with excluded samples should be realigned, or if I should simply exclude the rows in the alignment.
  
  I tried to figure out it by looking at the [Siddall and Whiting 1995](https://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.1999.tb00391.x) paper, which was referred to as the original description of this method in the chapter mentioned above. The best I found is
  
  > Using their alignment (<http://biology.unm.edu/esloker/>), when Polypodium is excluded, the most parsimonious tree groups the myxozoans as sister to the Bilateria (Fig. 1a).
  
  which makes me think that we should just exclude the taxa from the final alignment, but as there is still a space for interpretation, I thought I'll ask.
  
  **Tags:** phylogenetics, phylogeny
  
  > **Comments:**
  > **username_1**: In my opinion, since the aim of the SAW test and other leave-one-out approaches like it is to minimise the variance associated with any factor other than the taxon sampling, you should leave the alignment as-is and simply exclude the row of the associated taxon.  
  > **username_1**: Of course, things on long branches can often be annoyingly divergent and induce long internal INDELs and other weird alignment patterns. So I suspect it depends on exactly how much the homology statements in the alignment would change if you reinferred it dropping the taxon. Easiest way is just to try both (with realign, without realign) and compare.  
  > **username_0**: That's already quite close to an answer, thanks @username_1. (trying to subtly encourage you to write one)  
  > **username_2**: I agree more with @username_1's second comment. the idea of the test is to exclude all sources of information from the branch. Especially if the concern is long branches, the clustering that is implicit in the multiple alignment are likely to become nontrivial sources of information. One suspects also that choice of aligner (e.g. structure of initial heuristic steps) is also likely to interact with this.  
  
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  ## 0 answers
  
  