I used maximum likelihood method to draw the tree, i don't know why the bootstrap for the same bacterial species is low (1_29) as shown in the attachment (bootstrap consensus tree),and the numbers between the same species (original tree) are also low as you can see in the attachment. I used muscle algorithm for alignment my sequences by mega app for 16srRNA region. I also tried to use Gblock app, but the bootstrap is still the same. I appreciate your help.
I am guessing that the second tree is the bootstrap consensus tree which collapses any branches that have less than 50% bootstrap value (branches that appear in less than 50% of the trees generated by your bootstrap replicate sequences). I am a bit puzzled why the values are just the same when you run only the G Block sites.
@Patrice showers corneli
Bootstrap consensus tree is the 1st picture not the second one.
Also I tried UPGMA tree. All the branches which were 1 % till 29 % are changed to 100% as you can see in the attachment below.
But the node between species S and species sg and sf is left without bootstrap. Is this normal for UPGMA tree? And why?
For the UPGMA tree, the 100 bs value on sf,sg clade tells you that it is separated from su1 and everything else in the tree in 100% of the trees. It is the square format of the tree that makes it unclear. The 100 label would have meant the same thing if it had been attached the other end of the branch. su1 is a single terminal taxa and so has no bs value. It is not a clade.
But a UPGMA tree is not a good method because the branch lengths on the ML tree clearly do not follow molecular clock assumptions. So the 100% bootstrap values are meaningless on the UPGMA tree.
A lot of the branch lengths are zero or effectively zero, meaning that the sequences are the same as one another. For sequences s1-s11, only s11 differs from the others. Similarly s12 and s13 do not differ from one another and are only separated from s1-s11 with 18% bs confidence. on the other hand, s1-s13 are all separated from everything else in 100% of the bootstrap trees.
Let me know if that is not clear please.
Dear @Patrice Showers Corneli
thank you for your explanation, But I have some other question:
1. Why mega app construct 2 phyogenetic trees: Original tree (attachment no.1) and Bootstrap consensus tree (attachment NO. 2)
which one I can depend on?
2. When I construct a tree using ML is the
Hello dear, could anyone help me out please I really don't know how to remove these blue lines on my original tree MEGA X software, can anyone help many thanks in advance
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