4
$\begingroup$

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);
$\endgroup$
1
  • $\begingroup$ 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 at 14:23

2 Answers 2

5
$\begingroup$

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 I am very much out of date in this field and I haven't done anything like that in at least ten years, but back when I used to do it, my workflow was: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 
((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);
$\endgroup$
1
$\begingroup$

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.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.