<p><a href="https://i.sstatic.net/oXHWv.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/oXHWv.png" alt="enter image description here" /></a></p>
<p>Here's the result from <a href="http://tree.bio.ed.ac.uk/software/figtree/" rel="nofollow noreferrer">FigTree</a>. I thought there was a bug in the newick file, but it was fine.</p>
<p>I strongly recommend the answer by @terdon because there are other issues here, for example <code>111.16</code> value for the root and the <code>100.86</code> which occurs twice isn't cool.</p>
<p>I should have placed <code>monkey</code> as the outgroup, anyway just please ensure you do this for the report.</p>

CC BY-SA 4.0
2022-06-21T15:53:59.817Z
2022-06-21T18:25:52.133Z
2022-06-21T18:25:52.133Z
M__
<p>You will first need to align your sequences, and then feed the alignment to a program that can generate trees. I am very much out of date in this field and I haven't done anything like that in at least ten years, but back when I used to do it, my workflow was:</p>
<ol>
<li>Align the sequences using <a href="https://mafft.cbrc.jp/alignment/software/" rel="noreferrer">MAFFT</a> or <a href="https://tcoffee.crg.eu/" rel="noreferrer">t-coffee</a>.</li>
<li>Open the alignment in the <a href="https://www.jalview.org/" rel="noreferrer">Jalview alignment editor/viewer</a> which has options to generate the tree:</li>
</ol>
<p><a href="https://i.sstatic.net/UD3s3.png" rel="noreferrer"><img src="https://i.sstatic.net/UD3s3.png" alt="screenshot of jalview showing the &quot;calculate tree&quot; option" /></a></p>
<p>then just save the tree in Newick format:</p>
<p><a href="https://i.sstatic.net/1ZJBn.png" rel="noreferrer"><img src="https://i.sstatic.net/1ZJBn.png" alt="screenshot of jalview showing the file -&gt; save as Newick format option" /></a></p>
<p>The screenshots were taken using the default alignment provided by JalView itself, and this is the tree I got when I saved as Newick:</p>
<pre><code>$ cat tree 
((FER1_MESCR:24.484375,(((O80429_MAIZE:23.699999999999996,FER1_MAIZE:17.300000000000004):21.240625,(FER2_ARATH:13.067708333333336,((Q93Z60_ARATH:8.0,FER1_ARATH:8.0):8.401785714285715,(FER_BRANA:14.796875,FER3_RAPSA:8.203125):1.5982142857142847):0.9322916666666643):18.259375):9.75390625,((Q7XA98_TRIPR:24.8515625,FER1_PEA:27.1484375):6.643229166666671,((Q93XJ9_SOLTU:10.125,FER1_SOLLC:8.875):5.61363636363636,(FER_CAPAN:5.0,FER_CAPAA:0.0):19.38636363636364):20.48177083333333):8.97265625):9.52734375):20.2578125,FER1_SPIOL:20.2578125);
</code></pre>

CC BY-SA 4.0
2022-06-21T15:39:38.153Z
2022-06-21T15:39:38.153Z
terdon
<p>I have a set 189 taste receptor protein sequences (not aligned) in a fasta file. I like to get the phylogenetic tree in newick format. I was using earlier <a href="https://ngphylogeny.fr/" rel="nofollow noreferrer">https://ngphylogeny.fr/</a>. Unfortunately now it is not working due to some bugs. Necessarily, I just need newick information for the input fasta file.<br />
Any help would be highly appreciated.</p>
<p>Here is one newick example:</p>
<pre><code>((raccoon:19.19959,bear:6.80041):0.84600,
  ((sea_lion:11.99700, seal:12.00300):7.52973,  
     ((monkey:100.85930,cat:47.14069):20.59201,
       weasel:18.87953):2.09460):3.87382,
  dog:25.46154);
</code></pre>

CC BY-SA 4.0
2022-06-21T14:23:36.843Z
Please [edit] your question and add it there. Are these sequences of homologous genes? Entire genomes? Are they DNA? Protein? Are they already aligned to each other?
terdon
<phylogenetics>
Construct phylogeny from a Fasta file
# Construct phylogeny from a Fasta file

(Asked by: username_0 on 2022-06-21)

I have a set 189 taste receptor protein sequences (not aligned) in a fasta file. I like to get the phylogenetic tree in newick format. I was using earlier https://ngphylogeny.fr/. Unfortunately now it is not working due to some bugs. Necessarily, I just need newick information for the input fasta file.
Any help would be highly appreciated.
Here is one newick example:
((raccoon:19.19959,bear:6.80041):0.84600,
  ((sea_lion:11.99700, seal:12.00300):7.52973,  
     ((monkey:100.85930,cat:47.14069):20.59201,
       weasel:18.87953):2.09460):3.87382,
  dog:25.46154);

**Tags:** phylogenetics
> **Comments:**
> **username_1**: Please [edit] your question and add it there. Are these sequences of homologous genes? Entire genomes? Are they DNA? Protein? Are they already aligned to each other?  

---

## 2 answers

### Answer by username_1 on 2022-06-21. Score: 5 | Accepted answer

You will first need to align your sequences, and then feed the alignment to a program that can generate trees. I am very much out of date in this field and I haven't done anything like that in at least ten years, but back when I used to do it, my workflow was:

Align the sequences using MAFFT or t-coffee.
Open the alignment in the Jalview alignment editor/viewer which has options to generate the tree:


then just save the tree in Newick format:

The screenshots were taken using the default alignment provided by JalView itself, and this is the tree I got when I saved as Newick:
$ cat tree 
((FER1_MESCR:24.484375,(((O80429_MAIZE:23.699999999999996,FER1_MAIZE:17.300000000000004):21.240625,(FER2_ARATH:13.067708333333336,((Q93Z60_ARATH:8.0,FER1_ARATH:8.0):8.401785714285715,(FER_BRANA:14.796875,FER3_RAPSA:8.203125):1.5982142857142847):0.9322916666666643):18.259375):9.75390625,((Q7XA98_TRIPR:24.8515625,FER1_PEA:27.1484375):6.643229166666671,((Q93XJ9_SOLTU:10.125,FER1_SOLLC:8.875):5.61363636363636,(FER_CAPAN:5.0,FER_CAPAA:0.0):19.38636363636364):20.48177083333333):8.97265625):9.52734375):20.2578125,FER1_SPIOL:20.2578125);


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### Answer by username_2 on 2022-06-21. Score: 1

[![enter image description here](https://i.sstatic.net/oXHWv.png)](https://i.sstatic.net/oXHWv.png)

Here's the result from [FigTree](http://tree.bio.ed.ac.uk/software/figtree/). I thought there was a bug in the newick file, but it was fine.

I strongly recommend the answer by @terdon because there are other issues here, for example `111.16` value for the root and the `100.86` which occurs twice isn't cool.

I should have placed `monkey` as the outgroup, anyway just please ensure you do this for the report.


---

