Hello,
I am trying to construct phylogenetic tree of HIV-1. I downloaded sequences from few neighbor countries from Los Alamos HIV database. After aligning and trimming the length of sequences is usually 722 nucleotides. I can't trim less, because there are a lot of gaps within alignment file. When I construct Maximum Liklehood tree in FastTree or PhyML, the branches look very short. What could be a possible reason for it?
If 722 nucleotides length sequences can be used for constructing reliable phylogenetic tree?
Thank you!
The branch problem you mentioned does not relate to the sequence lengths you are using. Infact, the sequence length does not directly affect the branch lengths. And trimming the sequences will not help solving the branch length problem. To visualise the branches, you can try to use different visualization to manipulate branches try to toggle between cladogram/phylograms. And the branch length option from equal to proportional etc.
Abhijeet Singh thank you so much! I will try to do that. Also, another question is - If trimming is a crucial part when I use the FastTree? According to FastTree tutorial which I used, there is only alignment and tree construction steps. I could not find an answer to me question in the Internet.
Do not trim if you dont know what and how.
Just make sure before the alignment that you use correct sequences and of right lengths, without extra bases.
Correct sequences > alignment > tree construction > tree visualization.
You can also give it a try with the MEGA Platform.
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