Answers.Body: <p>Bootstrap values usually give you useful information, be they low or high. Usually, a "high" bootstrap value is something >= 70%. That means a clade is strongly supported; lower values are telling you the clade is not clearly separated from others. This could be for several reasons, e.g.:</p>
  
  <p>1) A subpopulation is not really separated from others, e.g. the viral sequences in  town "A" and town "B" are completely admixed, meaning the population is panmictic and there is continuous gene flow between the two of them;</p>
  
  <p>2) the populations diverged not long ago, it's too soon to have any phylogenetic signal, at least using the marker you are using (different genes evolve at different rates). Usually, housekeeping genes (which are usually very conserved) are used for populations that supposedly diverged long time ago.</p>
  
  <p>The interpretation of your tree should take into account the biology and epidemiology of your target organism. If you really want to learn more, I suggest a lot of reading, and definitely a class dedicated to molecular phylogenetics.</p>
  
  <p>This might be a good start:
  <a href="https://rads.stackoverflow.com/amzn/click/0521730716" rel="nofollow noreferrer">https://www.amazon.com/Phylogenetic-Handbook-Practical-Approach-Hypothesis/dp/0521730716</a></p>
  
  <p>Also, the NJ algorithm should allow for uneven branch lengths, maybe the tree you are showing is the consensus tree?</p>
  
  <p>Hope it helps</p>
  
  <p>Max</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-11-06T19:26:47.300Z
Answers.Text: The branch lengths are defaulted, however, they do allow different lengths based on how one would like them to look like. It's just a display function in UGENE. Thank you a lot for your comment, extremely helpful!
Answers.UserDisplayName: nazub
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-11-07T15:22:01.383Z
Answers.Text: You're welcome, and good luck. If you found the comment useful, please consider upvoting it or accepting it as answer.
Answers.UserDisplayName: Max_IT
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-28T21:03:56.690Z
Answers.Text: "the epidemiology" infers the bacteria are pathogenic.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-11-06T15:36:14.027Z
Answers.LastActivityDate: 2018-11-06T15:36:14.027Z
Answers.UserDisplayName: Max_IT
Body: <p>Dear knowledgeable bioinformaticians, I'm currently pursuing an undergraduate degree and as a result I do not have so much knowledge in this topic. I'm having some troubles understanding my phylogenetic three construction.</p>
  
  <p>For the construction of a phylogenetic tree UGENE was used. 11 homologous proteins from different species in the same genus/phyla were aligned. For the tree construction PHYLYP Neighbour Joining (NJ) with the distance matrix model “Jones-Taylor-Thornton” was used. Two trees were constructed, one without bootstrapping and one with bootstrapping (1000 pseudoreplicates). </p>
  
  <p>How do I interpret my values? Are they unusable since I have low bootstrap-values in a lot of my nodes? All guidance is appreciated, thank you.<a href="https://i.sstatic.net/P0WtG.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/P0WtG.png" alt="Without Bootstrap"></a> <a href="https://i.sstatic.net/H97tW.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/H97tW.png" alt="With Bootstrap"></a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-06T13:17:15.213Z
Comments.Text: Welcome to the site. Could you please clarify which one is without bootstrapping? It seems to be the one on the top, but I might be wrong
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-06T13:51:37.343Z
Comments.Text: Thank you! The upper one is not bootstrapped, the lower one is the bootstrapped one.
Comments.UserDisplayName: nazub
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-28T21:05:48.060Z
Comments.Text: Bootstrap values above 750 in the lower tree represent robust clades. Bootstraps above 800 are preferred and anything above 900 is strongly supported.
Comments.UserDisplayName: M__
Tags: <phylogeny><figure-explanation><phylogenetics>
Title: How do I interpret my phylogenetic tree construction from Glucosidases in the Actinobacteria class?
ThreadText: # How do I interpret my phylogenetic tree construction from Glucosidases in the Actinobacteria class?
  
  (Asked by: username_0 on 2018-11-06)
  
  Dear knowledgeable bioinformaticians, I'm currently pursuing an undergraduate degree and as a result I do not have so much knowledge in this topic. I'm having some troubles understanding my phylogenetic three construction.
  
  For the construction of a phylogenetic tree UGENE was used. 11 homologous proteins from different species in the same genus/phyla were aligned. For the tree construction PHYLYP Neighbour Joining (NJ) with the distance matrix model “Jones-Taylor-Thornton” was used. Two trees were constructed, one without bootstrapping and one with bootstrapping (1000 pseudoreplicates).
  
  How do I interpret my values? Are they unusable since I have low bootstrap-values in a lot of my nodes? All guidance is appreciated, thank you.[![Without Bootstrap](https://i.sstatic.net/P0WtG.png)](https://i.sstatic.net/P0WtG.png) [![With Bootstrap](https://i.sstatic.net/H97tW.png)](https://i.sstatic.net/H97tW.png)
  
  **Tags:** phylogeny, figure-explanation, phylogenetics
  
  > **Comments:**
  > **username_1**: Welcome to the site. Could you please clarify which one is without bootstrapping? It seems to be the one on the top, but I might be wrong  
  > **username_0**: Thank you! The upper one is not bootstrapped, the lower one is the bootstrapped one.  
  > **username_2**: Bootstrap values above 750 in the lower tree represent robust clades. Bootstraps above 800 are preferred and anything above 900 is strongly supported.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2018-11-06. Score: 2
  
  Bootstrap values usually give you useful information, be they low or high. Usually, a "high" bootstrap value is something >= 70%. That means a clade is strongly supported; lower values are telling you the clade is not clearly separated from others. This could be for several reasons, e.g.:
  
  1) A subpopulation is not really separated from others, e.g. the viral sequences in town "A" and town "B" are completely admixed, meaning the population is panmictic and there is continuous gene flow between the two of them;
  
  2) the populations diverged not long ago, it's too soon to have any phylogenetic signal, at least using the marker you are using (different genes evolve at different rates). Usually, housekeeping genes (which are usually very conserved) are used for populations that supposedly diverged long time ago.
  
  The interpretation of your tree should take into account the biology and epidemiology of your target organism. If you really want to learn more, I suggest a lot of reading, and definitely a class dedicated to molecular phylogenetics.
  
  This might be a good start:
  [https://www.amazon.com/Phylogenetic-Handbook-Practical-Approach-Hypothesis/dp/0521730716](https://rads.stackoverflow.com/amzn/click/0521730716)
  
  Also, the NJ algorithm should allow for uneven branch lengths, maybe the tree you are showing is the consensus tree?
  
  Hope it helps
  
  Max
  
  > **Comments:**
  > **username_0**: The branch lengths are defaulted, however, they do allow different lengths based on how one would like them to look like. It's just a display function in UGENE. Thank you a lot for your comment, extremely helpful!  
  > **username_3**: You're welcome, and good luck. If you found the comment useful, please consider upvoting it or accepting it as answer.  
  > **username_2**: "the epidemiology" infers the bacteria are pathogenic.  
  
  ---
  
  