Answers.Body: <p>Having thought this through, I think you've made a mistake. The file it wants is the outfile, you have given it the infile only. My original answer is below.</p>
  
  <p>====================</p>
  
  <p>From memory (my personal memory, not RAM, SSD or Stata), in the run command, you need to specify,</p>
  
  <pre><code>nruns=2
  </code></pre>
  
  <p>sumt will then combine both runs. If the file name is mystuff.run and nruns=2, there will be an output of mystuff.run1.t and mystuff.run2.t.</p>
  
  <p>If nruns isn't set then sumt will not work, or if the MCMCMC output ends up with different names again sumt will not work.</p>
  
  <p>With the burnin, you simply specify this in MrBayes. It is easy to write a script that will perform a 25% burnin. Tracer is nicely written, presumably C, its fast, but it has been around for a long time.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-14T21:50:07.910Z
Answers.LastActivityDate: 2018-12-17T22:25:04.760Z
Answers.LastEditDate: 2018-12-17T22:25:04.760Z
Answers.UserDisplayName: M__
Answers.Body: <p>This is a bit late. However, I am hoping someone else will find this useful since I had the same problem.</p>
  <p>The data matrix is your infile.nex file (the nex file you supplied for the analysis)</p>
  <ol>
  <li>Bracket out the mcmc command in your infile.nex
  <ul>
  <li>Prevents the file from being run again.</li>
  <li>May not be present.</li>
  </ul>
  </li>
  <li>In Mr. Bayes: Execute infile.nex
  <ul>
  <li>Loads you infile as the data matrix</li>
  </ul>
  </li>
  <li>In Mr. Bayes: sumt Filename=infile.nex nruns=2
  <ul>
  <li>If you have nruns set in you Mr. Bayes block you can skip this.</li>
  </ul>
  </li>
  </ol>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-02-28T23:39:02.237Z
Answers.LastActivityDate: 2021-02-28T23:39:02.237Z
Answers.UserDisplayName: Jeremy Buttler
Answers.Body: <p>This question was posted and answered as a <a href="https://github.com/NBISweden/MrBayes/issues/94" rel="nofollow noreferrer">Github Issue</a> in the MrBayes repository; I am copying the answer here for better visibility.</p>
  <hr />
  <blockquote>
  <p>Dear zillurbmb51,</p>
  <p>Thank you for your question. You need to load the data matrix in
  memory before issuing the <code>sumt</code> command, or in other words: &quot;A matrix
  must be specified before sumt can be used&quot;.</p>
  <p><strong>Example 1</strong> (where you haven't yet run a MCMC):</p>
  <p>Start mb, then type:</p>
  <pre><code>exe infile.nex
  mcmc
  sumt
  </code></pre>
  <p><strong>Example 2</strong> (where you already did a MCMC, and have <code>.t</code> files in your
  current working directory, and they are named <code>infile.nex.run1.t</code>,
  <code>infile.nex.run2.t</code>, etc):</p>
  <p>Start mb, then type:</p>
  <pre><code>exe infile.nex 
  sumt filename=infile.nex 
  </code></pre>
  <p>Cheers</p>
  <p>Johan</p>
  </blockquote>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-12-04T22:44:19.577Z
Answers.LastActivityDate: 2023-12-04T22:44:19.577Z
Answers.UserDisplayName: Harry Richman
Body: <h2>question 1</h2>
  <p>I wanted to use sumt command after completion of mcmc run. Whenever I use, <code>sumt Filename=infile.nex</code>, it gives me the error:</p>
  <pre><code>A matrix must be specified before sumt can be used
  Error when setting parameter &quot;Filename&quot; (1) 
  </code></pre>
  <p>But for the same analysis, I can use sump without any problem. What should I do now?</p>
  <h2>question 2</h2>
  <p>Another issue, I used burn in as 25% where as in Tracer, it is always showing 10%. No matter how much burn in I use, Tracer always shows 10% as burn in.</p>
  <h3>system stats</h3>
  <pre><code>Operating system : Centos7
  Version of MrBayes: 3.2.6
  </code></pre>
  <p>Thanks in advance,
  Best Regards,
  Zillur</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-13T08:00:33.320Z
Comments.Text: Hello zillur rahman,
  
  you've crossposted this question also on [biostars](https://www.biostars.org/p/354148/). You should mention this, so that everyone can see, if there is already an answers to your problem.
  
  Thanks.
  
  fin swimmer
Comments.UserDisplayName: finswimmer
Tags: <phylogenetics><phylogeny><mrbayes>
Title: mrbayes, Sumt ; Error when setting parameter "Filename" (1)
ThreadText: # mrbayes, Sumt ; Error when setting parameter "Filename" (1)
  
  (Asked by: username_0 on 2018-12-12)
  
  ## question 1
  
  I wanted to use sumt command after completion of mcmc run. Whenever I use, `sumt Filename=infile.nex`, it gives me the error:
  
  ```
  A matrix must be specified before sumt can be used
  Error when setting parameter "Filename" (1) 
  
  ```
  
  But for the same analysis, I can use sump without any problem. What should I do now?
  
  ## question 2
  
  Another issue, I used burn in as 25% where as in Tracer, it is always showing 10%. No matter how much burn in I use, Tracer always shows 10% as burn in.
  
  ### system stats
  
  ```
  Operating system : Centos7
  Version of MrBayes: 3.2.6
  
  ```
  
  Thanks in advance,
  Best Regards,
  username_0
  
  **Tags:** phylogenetics, phylogeny, mrbayes
  
  > **Comments:**
  > **username_1**: Hello username_0 username_0,  you've crossposted this question also on [biostars](https://www.biostars.org/p/354148/). You should mention this, so that everyone can see, if there is already an answers to your problem.  Thanks.  fin swimmer  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_2 on 2018-12-14. Score: 2
  
  Having thought this through, I think you've made a mistake. The file it wants is the outfile, you have given it the infile only. My original answer is below.
  
  ====================
  
  From memory (my personal memory, not RAM, SSD or Stata), in the run command, you need to specify,
  
  ```
  nruns=2
  
  ```
  
  sumt will then combine both runs. If the file name is mystuff.run and nruns=2, there will be an output of mystuff.run1.t and mystuff.run2.t.
  
  If nruns isn't set then sumt will not work, or if the MCMCMC output ends up with different names again sumt will not work.
  
  With the burnin, you simply specify this in MrBayes. It is easy to write a script that will perform a 25% burnin. Tracer is nicely written, presumably C, its fast, but it has been around for a long time.
  
  
  ---
  
  ### Answer by username_3 on 2021-02-28. Score: 1
  
  This is a bit late. However, I am hoping someone else will find this useful since I had the same problem.
  
  The data matrix is your infile.nex file (the nex file you supplied for the analysis)
  
  1. Bracket out the mcmc command in your infile.nex
     * Prevents the file from being run again.
     * May not be present.
  2. In Mr. Bayes: Execute infile.nex
     * Loads you infile as the data matrix
  3. In Mr. Bayes: sumt Filename=infile.nex nruns=2
     * If you have nruns set in you Mr. Bayes block you can skip this.
  
  
  ---
  
  ### Answer by username_4 on 2023-12-04. Score: 0
  
  This question was posted and answered as a [Github Issue](https://github.com/NBISweden/MrBayes/issues/94) in the MrBayes repository; I am copying the answer here for better visibility.
  
  ---
  
  > Dear zillurbmb51,
  >
  > Thank you for your question. You need to load the data matrix in
  > memory before issuing the `sumt` command, or in other words: "A matrix
  > must be specified before sumt can be used".
  >
  > **Example 1** (where you haven't yet run a MCMC):
  >
  > Start mb, then type:
  >
  > ```
  > exe infile.nex
  > mcmc
  > sumt
  >
  > ```
  >
  > **Example 2** (where you already did a MCMC, and have `.t` files in your
  > current working directory, and they are named `infile.nex.run1.t`,
  > `infile.nex.run2.t`, etc):
  >
  > Start mb, then type:
  >
  > ```
  > exe infile.nex 
  > sumt filename=infile.nex 
  >
  > ```
  >
  > Cheers
  >
  > Johan
  
  
  ---
  
  