# Construct phylogeny from a Fasta file

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);

• 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? Jun 21 at 14:23

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 I am very much out of date in this field and I haven't done anything like that in at least ten years, but back when I used to do it, my workflow was: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

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);


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.