Construct phylogeny from a Fasta file

Question

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);

Answer 1

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 I am very much out of date in this field and I haven't done anything like that in at least ten years, but back when I used to do it, my workflow was: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

Answer 2

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.