Answers.Body: <p>I second commenter Devon Ryan's suggestion, I'm just going to give a little more detail about how to do that. You can plug the BED files into the UCSC browser following these instructions: <a href="https://genome.ucsc.edu/goldenPath/help/customTrack.html" rel="nofollow noreferrer">https://genome.ucsc.edu/goldenPath/help/customTrack.html</a></p>
  
  <p>Now you can look at the overlap between your bed tracks (black boxes I believe) and conservation (red box).</p>
  
  <p><a href="https://i.sstatic.net/Fi3oz.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/Fi3oz.png" alt="enter image description here"></a></p>
  
  <p>Assuming that is all you want to do, that should do it. If you want to do further data analysis or processing, you can download the conservation track as a <code>.wib</code> file from UCSC. You can convert this file to BED as described <a href="http://genomewiki.cse.ucsc.edu/index.php/Using_hgWiggle_without_a_database" rel="nofollow noreferrer">here</a>, and use <a href="https://bedtools.readthedocs.io/en/latest/" rel="nofollow noreferrer">BEDTools</a> to analyze it together with your BED of regions of interest.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-20T10:27:03.157Z
Answers.Text: Hi and thanks for the answer. By doing this, i will find whatever correlation there is between these bed files (which by doing what you suggested i will find the regions that are conserved(?) ) and -some- diverse species with bedtools?
Answers.UserDisplayName: Jim Hat
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-20T16:48:57.090Z
Answers.Text: Hi @JimHat, it is a little hard to tell exactly what it is that you are supposed to do based on the question, the simple answer is "yes", you will look for overlaps between conserved regions and your regions of interest using commands like `bedtools intersect`. But I don't have a clear idea of what your goals are beyond that. Also, I looked a little deeper and the browser doesn't have BED files of the conserved regions but it does have `.wib` files, which can yield bed files. See updated answer.
Answers.UserDisplayName: Maximilian Press
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-09T21:06:32.623Z
Answers.LastActivityDate: 2020-04-20T16:50:12.580Z
Answers.LastEditDate: 2020-04-20T16:50:12.580Z
Answers.UserDisplayName: Maximilian Press
Body: <p>Hope everyone is well.</p>
  
  <p>So i was appointed with a task, and i need some guidance. Attention, the one that gave me the task may not have explained this very clearly. I will write what he exactly asked of me, and what he gave me as primary data.</p>
  
  <p>So he gave me 4 bed files (human genome) with chr and coordinates(start/stop), and asked me to do: "sequencing/coordinates conservation between diverse species".</p>
  
  <p>Is that doable with coordinates only or do i need sequences in fasta format (phast uses fasta format)? I just dont understand how i will find "conservation between diverse species" only with coordinates. It seems weird to me.</p>
  
  <p>I have found these programs: TargetOrtho2, Phast and BUSCO(?). Are they any good? Should i continue with one of them that you may have experience with?</p>
  
  <p>Thanks</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-08T11:55:27.200Z
Comments.Text: It is indeed a very unclear task. Are all the 4 bed files human bed files? What distant species you are interested in?
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-08T13:04:43.963Z
Comments.Text: Hi @JimHat That is cryptic, I think you need clarification! Literally that means non-humans.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-08T21:11:18.450Z
Comments.Text: I would suggest looking at those BED regions in the UCSC 100-way conservation tracks. Just doing that might just suffice.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-20T10:21:19.120Z
Comments.Text: hi all, and thanks for the answers! @KamilSJaron, yes they are bed files. He didnt clarify which distant species but i am guessing species that represent some taxonomy (or sub catergory of one, also maybe a model organism).
Comments.UserDisplayName: Jim Hat
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-20T10:22:03.960Z
Comments.Text: @DevonRyan i wll try that. Thanks
Comments.UserDisplayName: Jim Hat
Tags: <phylogenetics><phylogeny>
Title: Phylogenetics analysis between diverse species
ThreadText: # Phylogenetics analysis between diverse species
  
  (Asked by: username_0 on 2020-04-08)
  
  Hope everyone is well.
  
  So i was appointed with a task, and i need some guidance. Attention, the one that gave me the task may not have explained this very clearly. I will write what he exactly asked of me, and what he gave me as primary data.
  
  So he gave me 4 bed files (human genome) with chr and coordinates(start/stop), and asked me to do: "sequencing/coordinates conservation between diverse species".
  
  Is that doable with coordinates only or do i need sequences in fasta format (phast uses fasta format)? I just dont understand how i will find "conservation between diverse species" only with coordinates. It seems weird to me.
  
  I have found these programs: TargetOrtho2, Phast and BUSCO(?). Are they any good? Should i continue with one of them that you may have experience with?
  
  Thanks
  
  **Tags:** phylogenetics, phylogeny
  
  > **Comments:**
  > **username_1**: It is indeed a very unclear task. Are all the 4 bed files human bed files? What distant species you are interested in?  
  > **username_2**: Hi @username_0 That is cryptic, I think you need clarification! Literally that means non-humans.  
  > **username_3**: I would suggest looking at those BED regions in the UCSC 100-way conservation tracks. Just doing that might just suffice.  
  > **username_0**: hi all, and thanks for the answers! @username_1, yes they are bed files. He didnt clarify which distant species but i am guessing species that represent some taxonomy (or sub catergory of one, also maybe a model organism).  
  > **username_0**: @username_3 i wll try that. Thanks  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_4 on 2020-04-09. Score: 1
  
  I second commenter username_3 username_3's suggestion, I'm just going to give a little more detail about how to do that. You can plug the BED files into the UCSC browser following these instructions: <https://genome.ucsc.edu/goldenPath/help/customTrack.html>
  
  Now you can look at the overlap between your bed tracks (black boxes I believe) and conservation (red box).
  
  [![enter image description here](https://i.sstatic.net/Fi3oz.png)](https://i.sstatic.net/Fi3oz.png)
  
  Assuming that is all you want to do, that should do it. If you want to do further data analysis or processing, you can download the conservation track as a `.wib` file from UCSC. You can convert this file to BED as described [here](http://genomewiki.cse.ucsc.edu/index.php/Using_hgWiggle_without_a_database), and use [BEDTools](https://bedtools.readthedocs.io/en/latest/) to analyze it together with your BED of regions of interest.
  
  > **Comments:**
  > **username_0**: Hi and thanks for the answer. By doing this, i will find whatever correlation there is between these bed files (which by doing what you suggested i will find the regions that are conserved(?) ) and -some- diverse species with bedtools?  
  > **username_4**: Hi @username_0, it is a little hard to tell exactly what it is that you are supposed to do based on the question, the simple answer is "yes", you will look for overlaps between conserved regions and your regions of interest using commands like `bedtools intersect`. But I don't have a clear idea of what your goals are beyond that. Also, I looked a little deeper and the browser doesn't have BED files of the conserved regions but it does have `.wib` files, which can yield bed files. See updated answer.  
  
  ---
  
  