<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>

CC BY-SA 4.0
2020-07-13T09:32:38.630Z
Thank you, Max!! How do you think jaview[https://www.jalview.org/About]?
farinelli
CC BY-SA 4.0
2020-07-13T16:40:27.660Z
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.
Maximilian Press
CC BY-SA 4.0
2020-07-12T23:58:20.723Z
2020-07-12T23:58:20.723Z
Maximilian Press
<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>

CC BY-SA 4.0
2020-07-10T06:55:14.933Z
Why not use one of the many pair-wise alignment web tools? They tend to have nice graphical outputs like that.
Devon Ryan
CC BY-SA 4.0
2020-07-13T09:30:29.677Z
Thank you, which one is the best?
farinelli
CC BY-SA 4.0
2020-07-13T09:31:26.997Z
Just choose one, there is no best.
Devon Ryan
CC BY-SA 4.0
2020-07-13T09:33:51.813Z
OK, I'll use something.
farinelli
<phylogenetics>
Display a score or graph to visualize the degree of conservation of each residue from alignment data
# 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.  

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## 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 @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).

> **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.  

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