text: user4712: I would like to visualize tree with multiple sequence alignment. 
  My din.newick file is shown below,
  (org1:0.49999997,org2:0.47298786,org3:28.37858179);
  
  My din.fasta alignment file shown below,
  >org1
  ATGCTA
  >org2
  TAGCAT
  >org3
  AGTAGT
  
  I have tried the following code,
  library(tidyverse)
  library(ggtree) 
  library(seqinr)
  tree = read.tree("din.newick") 
  msaplot(p=ggtree(tree), fasta = "din.fasta")
  msaplot(p=ggtree(tree) + geom_tiplab(align=TRUE), fasta = "din.fasta")
  
  The above mentioned code is generating tree with the alignment matrix, but the tree root tip labels are not visible. It is either overlapped with matrix or it is not at all visible.  Kindly help me to fix this issue. 
  
  user181: You were very close, you just need to supply the offset argument to msaplot().
  So using your code block above with one extra argument in msaplot()
  library(tidyverse)
  library(ggtree) 
  library(seqinr)
  tree = read.tree("din.newick") 
  msaplot(p=ggtree(tree), fasta = "din.fasta")
  msaplot(p=ggtree(tree) + geom_tiplab(align=TRUE), fasta = "din.fasta", offset = 5)
  
  yields
  
  Thank you for supplying a minimal and reproducible example!
  
original_text: 4712: <p>I would like to visualize tree with multiple sequence alignment. 
  My <code>din.newick</code> file is shown below,</p>
  
  <pre><code>(org1:0.49999997,org2:0.47298786,org3:28.37858179);
  </code></pre>
  
  <p>My <code>din.fasta</code> alignment file shown below,</p>
  
  <pre><code>&gt;org1
  ATGCTA
  &gt;org2
  TAGCAT
  &gt;org3
  AGTAGT
  </code></pre>
  
  <p>I have tried the following code,</p>
  
  <pre><code>library(tidyverse)
  library(ggtree) 
  library(seqinr)
  tree = read.tree("din.newick") 
  msaplot(p=ggtree(tree), fasta = "din.fasta")
  msaplot(p=ggtree(tree) + geom_tiplab(align=TRUE), fasta = "din.fasta")
  </code></pre>
  
  <p>The above mentioned code is generating tree with the alignment matrix, but the tree root tip labels are not visible. It is either overlapped with matrix or it is not at all visible. <a href="https://i.stack.imgur.com/y9LbQ.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/y9LbQ.jpg" alt="msaplot(p=ggtree(tree) + geom_tiplab(align=TRUE), fasta = &quot;din.fasta&quot;)"></a> Kindly help me to fix this issue. </p>
   181: <p>You were very close, you just need to supply the <code>offset</code> argument to <code>msaplot()</code>.</p>
  
  <p>So using your code block above with one extra argument in <code>msaplot()</code></p>
  
  <pre><code>library(tidyverse)
  library(ggtree) 
  library(seqinr)
  tree = read.tree("din.newick") 
  msaplot(p=ggtree(tree), fasta = "din.fasta")
  msaplot(p=ggtree(tree) + geom_tiplab(align=TRUE), fasta = "din.fasta", offset = 5)
  </code></pre>
  
  <p>yields</p>
  
  <p><a href="https://i.stack.imgur.com/3thEk.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/3thEk.png" alt="msaplot with offset"></a></p>
  
  <p>Thank you for supplying a minimal and reproducible example!</p>
  