text: user14408: I have performed a phylogenetic analysis using CLUSTALW and obtained a phylogenetic tree. I know how to read a phylogenetic tree and how to relate the sequence similarity between two sequences by looking at the tree, but what I am concerned about is how one can decipher the father-daughter relationship by looking at the tree? Also, if I want to isolate the sequence of the father corresponding to a daughter sequence how can I do that?
  I have attached the corresponding image. In the image, I know that sequences "QXN18196" and "QXN18436" are closely related. But will it be safe to say that sequence "QXN18520" is the father sequence for both the sequences? Or if I want to establish a father-daughter relationship for the whole tree, what will be the relation between the sequences?
  
  user14409: Unless you have wildly differing mutation rates on different branches, you can't say that QXN18520 has the same sequence as the most recent common ancestor of QXN18196 and QXN18436, because QXN18520 was collected today, not back whenever QXN18196 and QXN18436 shared a common ancestor. All that you can say from this phylogeny is that there probably existed a common ancestor of QXN18196 and QXN18436, marked here by 5e-9[86.8], and that this common ancestor and QXN18520 shared a common ancestor even further back, marked here by 5e-9[0].
  (General observation: Note also that for a number of reasons, phylogenies often don't reflect reality -- they are simply a maximum likelihood estimate of the actual ancestral pedigree, often under some very unrealistic assumptions, and/or according to an incomplete or incorrect view of reality -- e.g. the samples that you have collected may have a lot of allele matches due to identity by state (IBS) rather than identity by descent (IBD). In other words, let phylogenies inform you, but don't assume they are the absolute truth.)
  
original_text: 14408: <p>I have performed a phylogenetic analysis using CLUSTALW and obtained a phylogenetic tree. I know how to read a phylogenetic tree and how to relate the sequence similarity between two sequences by looking at the tree, but what I am concerned about is how one can decipher the father-daughter relationship by looking at the tree? Also, if I want to isolate the sequence of the father corresponding to a daughter sequence how can I do that?
  I have attached the corresponding image. In the image, I know that sequences &quot;QXN18196&quot; and &quot;QXN18436&quot; are closely related. But will it be safe to say that sequence &quot;QXN18520&quot; is the father sequence for both the sequences? Or if I want to establish a father-daughter relationship for the whole tree, what will be the relation between the sequences?<a href="https://i.stack.imgur.com/4zKeX.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/4zKeX.png" alt="enter image description here" /></a></p>
   14409: <p>Unless you have wildly differing mutation rates on different branches, you can't say that QXN18520 has the same sequence as the most recent common ancestor of QXN18196 and QXN18436, because QXN18520 was collected today, not back whenever QXN18196 and QXN18436 shared a common ancestor. All that you can say from this phylogeny is that there probably existed a common ancestor of QXN18196 and QXN18436, marked here by 5e-9[86.8], and that this common ancestor and QXN18520 shared a common ancestor even further back, marked here by 5e-9[0].</p>
  <p>(General observation: Note also that for a number of reasons, phylogenies often don't reflect reality -- they are simply a maximum likelihood estimate of the actual ancestral pedigree, often under some very unrealistic assumptions, and/or according to an incomplete or incorrect view of reality -- e.g. the samples that you have collected may have a lot of allele matches due to identity by state (IBS) rather than identity by descent (IBD). In other words, let phylogenies inform you, but don't assume they are the absolute truth.)</p>
  