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:

  ((sea_lion:11.99700, seal:12.00300):7.52973,  
  • $\begingroup$ 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? $\endgroup$
    – terdon
    Jun 21, 2022 at 14:23

2 Answers 2


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 I am very much out of date in this field and I haven't done anything like that in at least ten years, but back when I used to do it, my workflow was:

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

screenshot of jalview showing the "calculate tree" option

then just save the tree in Newick format:

screenshot of jalview showing the file -> save as Newick format option

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 

enter image description here

Here's the result from 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.


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