Answers.Body: <p>I'd just use <a href="https://www.megasoftware.net" rel="nofollow noreferrer">MEGAX</a> (might be MEGA XI now), import the data and click &quot;proteins&quot; and &quot;alignment&quot;. You'll then go straight into its alignment editor, it will then permit you to either align or view and edit an aligned editor. I personally forget all the point and click options but there's a video here providing full instructions within the point and click environment: <a href="https://www.youtube.com/watch?v=8PfFqWnTVwI" rel="nofollow noreferrer">https://www.youtube.com/watch?v=8PfFqWnTVwI</a></p>
  <p>I'm happy to provide a walk-through here if required, because technically using offsite links is not encouraged.</p>
  <p>Jalview was never great, I had loads of trouble with it in its early days, and if you've having trouble using it I'd switch to something that does work. Obviously if you want to stick with Jalview, I can discard this post. BTW for Mac the GUI is Seqotron, which can outperforms Jalview and MEGA X, requirements depending.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-04-12T15:45:40.220Z
Answers.Text: Yeah, I was just going to use MEGAX, but since previously Jalview worked perfectly fine for me, I was curious, exactly what might have happened.
Answers.UserDisplayName: Tungstenas
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Answers.CreationDate: 2024-04-12T15:21:53.753Z
Answers.LastActivityDate: 2024-04-12T15:36:57.693Z
Answers.LastEditDate: 2024-04-12T15:36:57.693Z
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Answers.Body: <p>I will answer using what I can see in my Jalview but this is on a Linux machine and Jalview 2.11.2.0, I don't know how relevant this will be to you since you didn't tell us what version you are using.</p>
  <hr />
  <blockquote>
  <ol>
  <li>whenever I try to open a sequence file, Jalview instead loads the same MSA of sequences imported from UniProt, that I did not import myself;</li>
  </ol>
  </blockquote>
  <p>That's normal, as far as I know. It opens with some examples. I may not be remembering correctly, but I think this was the case already 15-20 years ago when I first tried Jalview. You can easily change this though, just go to Preferences =&gt; Visual and unclick the &quot;open file&quot; option:</p>
  <p><a href="https://i.sstatic.net/oWgW4.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/oWgW4.png" alt="screenshot of JalView preferences" /></a></p>
  <blockquote>
  <ol start="2">
  <li>I cannot find options to create a new file or open an existing one in 'file' section of taskbar nor anywhere else;</li>
  </ol>
  </blockquote>
  <p>I don't know about creating a new file, that isn't really what a &quot;viewer&quot; is for, but opening one should be File =&gt; Input alignment =&gt; From File:</p>
  <p><a href="https://i.sstatic.net/bePHt.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/bePHt.png" alt="screenshot of jalview and the import from file option" /></a></p>
  <blockquote>
  <ol start="3">
  <li>attempting to import sequences via 'file' &gt; 'add sequences' &gt; 'from textbox' just adds new sequences to the same defaultly loaded alignment file instead of creating a new one;</li>
  </ol>
  </blockquote>
  <p>I assume you are referring to the File menu inside the alignment window (1 in the image below). That is about <em>that</em> alignment, so of course, &quot;add sequences&quot; adds to that alignment. If you want to open a new file, you need the main File menu instead (2 in the image below):</p>
  <p><a href="https://i.sstatic.net/Xl0Ci.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/Xl0Ci.png" alt="screenshot of jalview showing the teo File menus" /></a></p>
  <blockquote>
  <ol start="4">
  <li>attempting to import sequences via 'file' &gt; 'add sequences' &gt; 'from file' runs into problem, that Jalview doesn't recognize .txt or .fasta files.</li>
  </ol>
  </blockquote>
  <p>I am not sure what you mean here, but neither of those extensions is common for alignment files. In any case, you might want to just change the extension it is looking for:</p>
  <p><a href="https://i.sstatic.net/xWFsg.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/xWFsg.png" alt="screenshot of the file open dialog with the place where you set the file type indicated" /></a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-04-12T18:11:09.457Z
Answers.Text: Thank you very much! Essentially, all the problems were caused by an example alignment, which would open instead of a file, that I was trying to open. As for .txt or .fasta files - I mainly use Jalview to open .fasta files with unaligned sequences and then use Jalview web services to create a MSA of those sequences, therefore being unable to open said files was frustrating.
Answers.UserDisplayName: Tungstenas
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-04-12T18:13:33.637Z
Answers.Text: Ah OK. I have only ever used it to open existing alignments, so that confused me @Tungstenas, but makes sense.
Answers.UserDisplayName: terdon
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Answers.CreationDate: 2024-04-12T17:05:05.590Z
Answers.LastActivityDate: 2024-04-12T17:05:05.590Z
Answers.UserDisplayName: terdon
Body: <p>I have encountered few problems regarding Jalview after updating my OS to Windows 11:</p>
  <ol>
  <li>whenever I try to open a sequence file, Jalview instead loads the
  same MSA of sequences imported from UniProt, that I did not import myself;</li>
  <li>I cannot find options to create a new file or open an existing one
  in 'file' section of taskbar nor anywhere else;</li>
  <li>attempting to import
  sequences via 'file' &gt; 'add sequences' &gt; 'from textbox' just adds
  new sequences to the same defaultly loaded alignment file instead of
  creating a new one;</li>
  <li>attempting to import sequences via 'file' &gt; 'add
  sequences' &gt; 'from file' runs into problem, that Jalview doesn't
  recognize .txt or .fasta files.</li>
  </ol>
  <p>My current version of Jalview is 2.11.3.2. I tried uninstalling and reinstalling the program and made sure it is associated with .txt and .fasta extensions.</p>
  <p>What issues may I be facing here? And in general, why is an interface of Jalview so different after a Windows update? (I remember options to create new files or open them existing in program's dialogue previously, also there was never a 'default alignment' that loads every time when starting the app).</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-12T14:53:39.453Z
Comments.Text: No, I don't have access to Mac OR and I am loading just 6 protein sequences.
Comments.UserDisplayName: Tungstenas
Tags: <windows>
Title: Jalview interface issues
ThreadText: # Jalview interface issues
  
  (Asked by: username_0 on 2024-04-12)
  
  I have encountered few problems regarding Jalview after updating my OS to Windows 11:
  
  1. whenever I try to open a sequence file, Jalview instead loads the
     same MSA of sequences imported from UniProt, that I did not import myself;
  2. I cannot find options to create a new file or open an existing one
     in 'file' section of taskbar nor anywhere else;
  3. attempting to import
     sequences via 'file' > 'add sequences' > 'from textbox' just adds
     new sequences to the same defaultly loaded alignment file instead of
     creating a new one;
  4. attempting to import sequences via 'file' > 'add
     sequences' > 'from file' runs into problem, that Jalview doesn't
     recognize .txt or .fasta files.
  
  My current version of Jalview is 2.11.3.2. I tried uninstalling and reinstalling the program and made sure it is associated with .txt and .fasta extensions.
  
  What issues may I be facing here? And in general, why is an interface of Jalview so different after a Windows update? (I remember options to create new files or open them existing in program's dialogue previously, also there was never a 'default alignment' that loads every time when starting the app).
  
  **Tags:** windows
  
  > **Comments:**
  > **username_0**: No, I don't have access to Mac OR and I am loading just 6 protein sequences.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2024-04-12. Score: 0
  
  I'd just use [MEGAX](https://www.megasoftware.net) (might be MEGA XI now), import the data and click "proteins" and "alignment". You'll then go straight into its alignment editor, it will then permit you to either align or view and edit an aligned editor. I personally forget all the point and click options but there's a video here providing full instructions within the point and click environment: <https://www.youtube.com/watch?v=8PfFqWnTVwI>
  
  I'm happy to provide a walk-through here if required, because technically using offsite links is not encouraged.
  
  Jalview was never great, I had loads of trouble with it in its early days, and if you've having trouble using it I'd switch to something that does work. Obviously if you want to stick with Jalview, I can discard this post. BTW for Mac the GUI is Seqotron, which can outperforms Jalview and MEGA X, requirements depending.
  
  > **Comments:**
  > **username_0**: Yeah, I was just going to use MEGAX, but since previously Jalview worked perfectly fine for me, I was curious, exactly what might have happened.  
  
  ---
  
  ### Answer by username_2 on 2024-04-12. Score: 0
  
  I will answer using what I can see in my Jalview but this is on a Linux machine and Jalview 2.11.2.0, I don't know how relevant this will be to you since you didn't tell us what version you are using.
  
  ---
  
  > 1. whenever I try to open a sequence file, Jalview instead loads the same MSA of sequences imported from UniProt, that I did not import myself;
  
  That's normal, as far as I know. It opens with some examples. I may not be remembering correctly, but I think this was the case already 15-20 years ago when I first tried Jalview. You can easily change this though, just go to Preferences => Visual and unclick the "open file" option:
  
  [![screenshot of JalView preferences](https://i.sstatic.net/oWgW4.png)](https://i.sstatic.net/oWgW4.png)
  
  > 2. I cannot find options to create a new file or open an existing one in 'file' section of taskbar nor anywhere else;
  
  I don't know about creating a new file, that isn't really what a "viewer" is for, but opening one should be File => Input alignment => From File:
  
  [![screenshot of jalview and the import from file option](https://i.sstatic.net/bePHt.png)](https://i.sstatic.net/bePHt.png)
  
  > 3. attempting to import sequences via 'file' > 'add sequences' > 'from textbox' just adds new sequences to the same defaultly loaded alignment file instead of creating a new one;
  
  I assume you are referring to the File menu inside the alignment window (1 in the image below). That is about *that* alignment, so of course, "add sequences" adds to that alignment. If you want to open a new file, you need the main File menu instead (2 in the image below):
  
  [![screenshot of jalview showing the teo File menus](https://i.sstatic.net/Xl0Ci.png)](https://i.sstatic.net/Xl0Ci.png)
  
  > 4. attempting to import sequences via 'file' > 'add sequences' > 'from file' runs into problem, that Jalview doesn't recognize .txt or .fasta files.
  
  I am not sure what you mean here, but neither of those extensions is common for alignment files. In any case, you might want to just change the extension it is looking for:
  
  [![screenshot of the file open dialog with the place where you set the file type indicated](https://i.sstatic.net/xWFsg.png)](https://i.sstatic.net/xWFsg.png)
  
  > **Comments:**
  > **username_0**: Thank you very much! Essentially, all the problems were caused by an example alignment, which would open instead of a file, that I was trying to open. As for .txt or .fasta files - I mainly use Jalview to open .fasta files with unaligned sequences and then use Jalview web services to create a MSA of those sequences, therefore being unable to open said files was frustrating.  
  > **username_2**: Ah OK. I have only ever used it to open existing alignments, so that confused me @username_0, but makes sense.  
  
  ---
  
  