Answers.Body: <p>Anyway the chances are this is gene duplication. It will be a housekeeping type gene or else histone that sort of thing. You simply map the different genes onto the various metazoan classes. In your case nematodes and arthropods are basal metazoan, so their is correct given the clade they form part of all all representatives is that gene.</p>
  
  <p>There is nothing weird you just need to read the deep phylogeneticists work like Tom Caveliar-Smith and Sandy Balfour, possibly Blair-Hedges</p>
  
  <p>There are alot of eukaryotes prior to the invertebrates, just look at the Cambrian explosion</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-29T16:23:19.607Z
Answers.Text: How about the tri-furcation at the branch giving rise to RFX5-RFX7, Smed  RFX15486 and Dmel Uncharacterized...? Isn't there a problem there?
Answers.UserDisplayName: haci
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-29T16:53:16.417Z
Answers.Text: No, its simply a polytomy, increase the amount of data and resolution will sharpen to a bifurcation. From recollection the arthropod - worm boundary isn't well resolved. Might have changed with genome availability
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-30T13:10:56.507Z
Answers.Text: I think Blair-Hedges was the person most related to this
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-29T15:56:15.093Z
Answers.LastActivityDate: 2019-09-29T15:56:15.093Z
Answers.UserDisplayName: M__
Body: <p>I am required to create a phylogenetic tree(s) of my genes of interest and am currently blasting (tblastn) my genes of interest from S. mediterranea against model systems before expanding my search.</p>
  <p><strong>Problem</strong> I get something like the attached which does not look like right. What am I doing wrong? I'm aligning via MUSCLE, and running Maximum Likliehood Protein models and consequentially, using the correct model (JTT, for instance). <a href="https://i.sstatic.net/0RAuH.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/0RAuH.png" alt="enter image description here" /></a></p>
  <p>Greatly appreciate any help in advance.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-29T10:00:11.087Z
Comments.Text: Which gene is it?
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-29T10:17:30.613Z
Comments.Text: Anyway yes it's possible, I'm confused by your Tblastn because that will give nucleotides, JTT is s protein model
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-29T10:47:28.993Z
Comments.Text: @MichaelG. tblastn gives protein, not nucleotide. It takes a protein query and blasts it against a translated nucleotide database. The results are protein alignments.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-29T10:48:30.950Z
Comments.Text: @zaci, could you explain what looks wrong? Why would there be something wrong here? You seem to be aligning small parts of each protein, so it makes sense that you're not finding the "real" species tree.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-29T11:23:34.030Z
Comments.Text: I suspect it's gene duplication. Helminths and insects are in the right place as basal metazoa
Comments.UserDisplayName: M__
Tags: <phylogenetics><fasta><phylogeny><systems-biology>
Title: Weird phylogenetic tree
ThreadText: # Weird phylogenetic tree
  
  (Asked by: username_0 on 2019-09-29)
  
  I am required to create a phylogenetic tree(s) of my genes of interest and am currently blasting (tblastn) my genes of interest from S. mediterranea against model systems before expanding my search.
  
  **Problem** I get something like the attached which does not look like right. What am I doing wrong? I'm aligning via MUSCLE, and running Maximum Likliehood Protein models and consequentially, using the correct model (JTT, for instance). [![enter image description here](https://i.sstatic.net/0RAuH.png)](https://i.sstatic.net/0RAuH.png)
  
  Greatly appreciate any help in advance.
  
  **Tags:** phylogenetics, fasta, phylogeny, systems-biology
  
  > **Comments:**
  > **username_1**: Which gene is it?  
  > **username_1**: Anyway yes it's possible, I'm confused by your Tblastn because that will give nucleotides, JTT is s protein model  
  > **username_2**: @MichaelG. tblastn gives protein, not nucleotide. It takes a protein query and blasts it against a translated nucleotide database. The results are protein alignments.  
  > **username_2**: @username_0, could you explain what looks wrong? Why would there be something wrong here? You seem to be aligning small parts of each protein, so it makes sense that you're not finding the "real" species tree.  
  > **username_1**: I suspect it's gene duplication. Helminths and insects are in the right place as basal metazoa  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-09-29. Score: 2
  
  Anyway the chances are this is gene duplication. It will be a housekeeping type gene or else histone that sort of thing. You simply map the different genes onto the various metazoan classes. In your case nematodes and arthropods are basal metazoan, so their is correct given the clade they form part of all all representatives is that gene.
  
  There is nothing weird you just need to read the deep phylogeneticists work like Tom Caveliar-Smith and Sandy Balfour, possibly Blair-Hedges
  
  There are alot of eukaryotes prior to the invertebrates, just look at the Cambrian explosion
  
  > **Comments:**
  > **username_3**: How about the tri-furcation at the branch giving rise to RFX5-RFX7, Smed  RFX15486 and Dmel Uncharacterized...? Isn't there a problem there?  
  > **username_1**: No, its simply a polytomy, increase the amount of data and resolution will sharpen to a bifurcation. From recollection the arthropod - worm boundary isn't well resolved. Might have changed with genome availability  
  > **username_1**: I think Blair-Hedges was the person most related to this  
  
  ---
  
  