Answers.Body: <p>I would suggest a <a href="https://weblogo.berkeley.edu/logo.cgi" rel="nofollow noreferrer">logo plot</a>, e.g.:
  <a href="https://i.sstatic.net/Udws0.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/Udws0.png" alt="https://weblogo.berkeley.edu/examples.html" /></a></p>
  <p>I would take @Devon Ryan's suggestion to create a multiple sequence alignment (MSA), and plug that into that logo plot tool (or others, there are many like it).</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-13T09:32:38.630Z
Answers.Text: Thank you, Max!! How do you think jaview[https://www.jalview.org/About]?
Answers.UserDisplayName: farinelli
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-13T16:40:27.660Z
Answers.Text: I have never used JalView but the tutorial says that it has this feature (http://www.jalview.org/tutorial/TheJalviewTutorial.pdf, p.44). I like to use smaller, simpler tools but if you like JalView it should work for making a logo plot.
Answers.UserDisplayName: Maximilian Press
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-12T23:58:20.723Z
Answers.LastActivityDate: 2020-07-12T23:58:20.723Z
Answers.UserDisplayName: Maximilian Press
Body: <p>I would like to display a score or graph to visualize the degree of conservation of each residue from the amino acid alignment data.
  If possible, I'd like to extract the parts of the game that scored above a certain level.</p>
  <p>Is there a tool or source code (python) to do that?</p>
  <p>Sorry for my bad English ...</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-10T06:55:14.933Z
Comments.Text: Why not use one of the many pair-wise alignment web tools? They tend to have nice graphical outputs like that.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-13T09:30:29.677Z
Comments.Text: Thank you, which one is the best?
Comments.UserDisplayName: farinelli
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-13T09:31:26.997Z
Comments.Text: Just choose one, there is no best.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-13T09:33:51.813Z
Comments.Text: OK, I'll use something.
Comments.UserDisplayName: farinelli
Tags: <phylogenetics>
Title: Display a score or graph to visualize the degree of conservation of each residue from alignment data
ThreadText: # Display a score or graph to visualize the degree of conservation of each residue from alignment data
  
  (Asked by: username_0 on 2020-07-10)
  
  I would like to display a score or graph to visualize the degree of conservation of each residue from the amino acid alignment data.
  If possible, I'd like to extract the parts of the game that scored above a certain level.
  
  Is there a tool or source code (python) to do that?
  
  Sorry for my bad English ...
  
  **Tags:** phylogenetics
  
  > **Comments:**
  > **username_1**: Why not use one of the many pair-wise alignment web tools? They tend to have nice graphical outputs like that.  
  > **username_0**: Thank you, which one is the best?  
  > **username_1**: Just choose one, there is no best.  
  > **username_0**: OK, I'll use something.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2020-07-12. Score: 1
  
  I would suggest a [logo plot](https://weblogo.berkeley.edu/logo.cgi), e.g.:
  [![https://weblogo.berkeley.edu/examples.html](https://i.sstatic.net/Udws0.png)](https://i.sstatic.net/Udws0.png)
  
  I would take @username_1's suggestion to create a multiple sequence alignment (MSA), and plug that into that logo plot tool (or others, there are many like it).
  
  > **Comments:**
  > **username_0**: Thank you, Max!! How do you think jaview[https://www.jalview.org/About]?  
  > **username_2**: I have never used JalView but the tutorial says that it has this feature (http://www.jalview.org/tutorial/TheJalviewTutorial.pdf, p.44). I like to use smaller, simpler tools but if you like JalView it should work for making a logo plot.  
  
  ---
  
  