Answers.Body: <p>The problem with the tree format presented is that it does not conform to a known standard. Whilst its possible to write a parser I don't think its a good idea.</p>
  <p>This output is hierarchical clustering, UPGMA, that sort of thing. Its not phylogenetics because this is a linkage tree.</p>
  <p>Can you access the distance matrix prior to the clustering? If so the information below the line will help.</p>
  <p>The output should provide the raw distance matrix prior to hierarchical clustering and will certainly have generated it in the calculation. BTW that particular clustering method isn't cool compared with nj (below) for complex reasons.</p>
  <p>The calculation will be:</p>
  <ol>
  <li>Perform pairwise linkage analysis</li>
  <li>Perform cluster analysis on the resulting matrix</li>
  </ol>
  <hr />
  <p>You need neighbor-joining to convert the distance matrix into a newick-format. There is no possibility of a direct conversion.</p>
  <p>If you are using <code>R</code> its in the <code>ape</code> library via
  <code>treenk &lt;- nj(M)</code> with <code>M</code> is the matrix. The treenk will be a format that can be read straight into <code>ggtree</code></p>
  <p>Briefly, a distance matrix requires a clustering algorithm and neighbor-joining is by far the best clustering method developed in phylogenetics.</p>
  <p>The following is a phylogenetics example ... this is different from the example you have 'cause thats about linkage.</p>
  <pre><code>data(mynucleotides)
  tr &lt;- nj(dist.dna(mynucleotides))
  plot(tr)
  </code></pre>
  <p>I your case the final line will be something like <code>ggtree(tr)</code> ... with various options.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-11-12T17:06:35.873Z
Answers.Text: Thank for the idea. It helps so much.
Answers.UserDisplayName: SuleymanSelim
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-11-11T20:13:32.717Z
Answers.LastActivityDate: 2022-11-12T12:09:59.023Z
Answers.LastEditDate: 2022-11-12T12:09:59.023Z
Answers.UserDisplayName: M__
Body: <p>I have pairwise distance data for single linkage cluster and I would like to convert it to <a href="http://en.wikipedia.org/wiki/Newick_format" rel="nofollow noreferrer">newick format</a>.</p>
  <p>I was unable to find a conversion algorithm.</p>
  <p>I require newick format for visualization and annotation of a phylogeny.</p>
  <p>Here is the output.</p>
  <pre><code>INFO  : ======================================
  INFO  : Pairwise single linkage clustering
  INFO  : ======================================
  INFO  : Hierarchical Tree
  INFO  : ======================================
  INFO  : Node     Item 1   Item 2      Distance
  INFO  :     0 :       53       52        0.001  5zxf  5z02
  INFO  :    -1 :       64       60        0.002  7bj6  7bir
  INFO  :    -2 :       62       -1        0.002  7biv          
  INFO  :    -3 :       34       26        0.002  4wt2  4ode
  INFO  :    -4 :       65       -2        0.003  7bmg          
  INFO  :    -5 :       25       13        0.003  4occ  4erf
  INFO  :    -6 :       29       -3        0.009  4ogt          
  INFO  :    -7 :       39       38        0.010  4zyi  4zyf
  INFO  :    -8 :       50       48        0.011  5oc8  5ln2
  INFO  :    -9 :       54       -8        0.012  6ggn          
  INFO  :   -10 :       42       41        0.015  5hmi  5hmh
  INFO  :   -11 :       -4       61        0.020            7bit
  INFO  :   -12 :       70       40        0.028  7qdq  5c5a
  INFO  :   -13 :       47       68        0.032  5laz  7na3
  INFO  :   -14 :       -9       45        0.035            5law
  INFO  :   -15 :       49       59        0.038  5oai  6q9o
  INFO  :   -16 :       32       -5        0.039  4qo4          
  INFO  :   -17 :      -15        8        0.044            3uu1
  INFO  :   -18 :       23      -16        0.047  4oas          
  INFO  :   -19 :      -14       -7        0.053                    
  INFO  :   -20 :       24      -18        0.057  4oba          
  INFO  :   -21 :      -19        6        0.057            3lbl
  INFO  :   -22 :       43      -10        0.058  5hmk          
  INFO  :   -23 :       44       19        0.059  5lav  4jvr
  INFO  :   -24 :      -23      -20        0.061                    
  INFO  :   -25 :      -11       15        0.061            4hg7
  INFO  :   -26 :       57      -24        0.062  6q9h          
  INFO  :   -27 :       27       -6        0.065  4odf          
  INFO  :   -28 :      -25      -17        0.067                    
  INFO  :   -29 :       14      -28        0.067  4hbm          
  INFO  :   -30 :      -13      -21        0.067                    
  INFO  :   -31 :      -27      -29        0.067                    
  INFO  :   -32 :      -26      -30        0.068                    
  INFO  :   -33 :       58       21        0.068  6q9l  4mdn
  INFO  :   -34 :      -31      -32        0.070                    
  INFO  :   -35 :       17        5        0.071  4jv9  3lbk
  INFO  :   -36 :       30      -34        0.074  4ogv          
  INFO  :   -37 :      -33        2        0.077            1t4e
  INFO  :   -38 :       35      -36        0.079  4zfi          
  INFO  :   -39 :       20      -38        0.086  4jwr          
  INFO  :   -40 :      -39      -37        0.094                    
  INFO  :   -41 :        7      -40        0.106  3tj2          
  INFO  :   -42 :       51      -41        0.111  5trf          
  INFO  :   -43 :       69      -42        0.112  7na4          
  INFO  :   -44 :       56      -43        0.113  6q96          
  INFO  :   -45 :        4      -44        0.127  3jzk          
  INFO  :   -46 :       33      -45        0.129  4qoc          
  INFO  :   -47 :       22      -46        0.137  4mdq          
  INFO  :   -48 :      -12      -47        0.151                    
  INFO  :   -49 :       37      -48        0.155  4zyc          
  INFO  :   -50 :       31      -49        0.156  4oq3          
  INFO  :   -51 :       12      -50        0.158  4ere          
  INFO  :   -52 :      -22       46        0.161            5lay
  INFO  :   -53 :      -35      -51        0.182                    
  INFO  :   -54 :       55      -53        0.186  6i29          
  INFO  :   -55 :       10      -54        0.224  3w69          
  INFO  :   -56 :       18      -55        0.238  4jve          
  INFO  :   -57 :        9      -56        0.265  3vzv          
  INFO  :   -58 :       28      -57        0.271  4ogn          
  INFO  :   -59 :      -58        1        1.000            1rv1
  INFO  :   -60 :       66      -59        1.000  7na1          
  INFO  :   -61 :        0      -60        1.000                    
  INFO  :   -62 :      -52      -61        1.000                    
  INFO  :   -63 :       11      -62        1.000  4dij          
  INFO  :   -64 :       67      -63        1.000  7na2          
  INFO  :   -65 :       16      -64        1.000  4jv7          
  INFO  :   -66 :       36      -65        1.000  4zgk          
  INFO  :   -67 :        3      -66        1.000  2lzg          
  </code></pre>
  
Tags: <phylogenetics><phylogeny><ggtree>
Title: Converting Pairwise single- linkage clustering distance data to "newick" format
ThreadText: # Converting Pairwise single- linkage clustering distance data to "newick" format
  
  (Asked by: username_0 on 2022-11-11)
  
  I have pairwise distance data for single linkage cluster and I would like to convert it to [newick format](http://en.wikipedia.org/wiki/Newick_format).
  
  I was unable to find a conversion algorithm.
  
  I require newick format for visualization and annotation of a phylogeny.
  
  Here is the output.
  
  ```
  INFO  : ======================================
  INFO  : Pairwise single linkage clustering
  INFO  : ======================================
  INFO  : Hierarchical Tree
  INFO  : ======================================
  INFO  : Node     Item 1   Item 2      Distance
  INFO  :     0 :       53       52        0.001  5zxf  5z02
  INFO  :    -1 :       64       60        0.002  7bj6  7bir
  INFO  :    -2 :       62       -1        0.002  7biv          
  INFO  :    -3 :       34       26        0.002  4wt2  4ode
  INFO  :    -4 :       65       -2        0.003  7bmg          
  INFO  :    -5 :       25       13        0.003  4occ  4erf
  INFO  :    -6 :       29       -3        0.009  4ogt          
  INFO  :    -7 :       39       38        0.010  4zyi  4zyf
  INFO  :    -8 :       50       48        0.011  5oc8  5ln2
  INFO  :    -9 :       54       -8        0.012  6ggn          
  INFO  :   -10 :       42       41        0.015  5hmi  5hmh
  INFO  :   -11 :       -4       61        0.020            7bit
  INFO  :   -12 :       70       40        0.028  7qdq  5c5a
  INFO  :   -13 :       47       68        0.032  5laz  7na3
  INFO  :   -14 :       -9       45        0.035            5law
  INFO  :   -15 :       49       59        0.038  5oai  6q9o
  INFO  :   -16 :       32       -5        0.039  4qo4          
  INFO  :   -17 :      -15        8        0.044            3uu1
  INFO  :   -18 :       23      -16        0.047  4oas          
  INFO  :   -19 :      -14       -7        0.053                    
  INFO  :   -20 :       24      -18        0.057  4oba          
  INFO  :   -21 :      -19        6        0.057            3lbl
  INFO  :   -22 :       43      -10        0.058  5hmk          
  INFO  :   -23 :       44       19        0.059  5lav  4jvr
  INFO  :   -24 :      -23      -20        0.061                    
  INFO  :   -25 :      -11       15        0.061            4hg7
  INFO  :   -26 :       57      -24        0.062  6q9h          
  INFO  :   -27 :       27       -6        0.065  4odf          
  INFO  :   -28 :      -25      -17        0.067                    
  INFO  :   -29 :       14      -28        0.067  4hbm          
  INFO  :   -30 :      -13      -21        0.067                    
  INFO  :   -31 :      -27      -29        0.067                    
  INFO  :   -32 :      -26      -30        0.068                    
  INFO  :   -33 :       58       21        0.068  6q9l  4mdn
  INFO  :   -34 :      -31      -32        0.070                    
  INFO  :   -35 :       17        5        0.071  4jv9  3lbk
  INFO  :   -36 :       30      -34        0.074  4ogv          
  INFO  :   -37 :      -33        2        0.077            1t4e
  INFO  :   -38 :       35      -36        0.079  4zfi          
  INFO  :   -39 :       20      -38        0.086  4jwr          
  INFO  :   -40 :      -39      -37        0.094                    
  INFO  :   -41 :        7      -40        0.106  3tj2          
  INFO  :   -42 :       51      -41        0.111  5trf          
  INFO  :   -43 :       69      -42        0.112  7na4          
  INFO  :   -44 :       56      -43        0.113  6q96          
  INFO  :   -45 :        4      -44        0.127  3jzk          
  INFO  :   -46 :       33      -45        0.129  4qoc          
  INFO  :   -47 :       22      -46        0.137  4mdq          
  INFO  :   -48 :      -12      -47        0.151                    
  INFO  :   -49 :       37      -48        0.155  4zyc          
  INFO  :   -50 :       31      -49        0.156  4oq3          
  INFO  :   -51 :       12      -50        0.158  4ere          
  INFO  :   -52 :      -22       46        0.161            5lay
  INFO  :   -53 :      -35      -51        0.182                    
  INFO  :   -54 :       55      -53        0.186  6i29          
  INFO  :   -55 :       10      -54        0.224  3w69          
  INFO  :   -56 :       18      -55        0.238  4jve          
  INFO  :   -57 :        9      -56        0.265  3vzv          
  INFO  :   -58 :       28      -57        0.271  4ogn          
  INFO  :   -59 :      -58        1        1.000            1rv1
  INFO  :   -60 :       66      -59        1.000  7na1          
  INFO  :   -61 :        0      -60        1.000                    
  INFO  :   -62 :      -52      -61        1.000                    
  INFO  :   -63 :       11      -62        1.000  4dij          
  INFO  :   -64 :       67      -63        1.000  7na2          
  INFO  :   -65 :       16      -64        1.000  4jv7          
  INFO  :   -66 :       36      -65        1.000  4zgk          
  INFO  :   -67 :        3      -66        1.000  2lzg          
  
  ```
  
  **Tags:** phylogenetics, phylogeny, ggtree
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-11-11. Score: 2 | Accepted answer
  
  The problem with the tree format presented is that it does not conform to a known standard. Whilst its possible to write a parser I don't think its a good idea.
  
  This output is hierarchical clustering, UPGMA, that sort of thing. Its not phylogenetics because this is a linkage tree.
  
  Can you access the distance matrix prior to the clustering? If so the information below the line will help.
  
  The output should provide the raw distance matrix prior to hierarchical clustering and will certainly have generated it in the calculation. BTW that particular clustering method isn't cool compared with nj (below) for complex reasons.
  
  The calculation will be:
  
  1. Perform pairwise linkage analysis
  2. Perform cluster analysis on the resulting matrix
  
  ---
  
  You need neighbor-joining to convert the distance matrix into a newick-format. There is no possibility of a direct conversion.
  
  If you are using `R` its in the `ape` library via
  `treenk <- nj(M)` with `M` is the matrix. The treenk will be a format that can be read straight into `ggtree`
  
  Briefly, a distance matrix requires a clustering algorithm and neighbor-joining is by far the best clustering method developed in phylogenetics.
  
  The following is a phylogenetics example ... this is different from the example you have 'cause thats about linkage.
  
  ```
  data(mynucleotides)
  tr <- nj(dist.dna(mynucleotides))
  plot(tr)
  
  ```
  
  I your case the final line will be something like `ggtree(tr)` ... with various options.
  
  > **Comments:**
  > **username_0**: Thank for the idea. It helps so much.  
  
  ---
  
  