I made this tree using samples of the same species via MEGA using Maximum Liklihood method and Bootstrap values. I am still unsure what bootstrap values mean in this case and why samples have zero-length branches? Please help analyze this tree thanks!
The choice of your out-group does not looks appropriate. Is very different from the rest of the branches that why the branch lengths of your main tree are invisible. Thus, you need to reconsider the out group. Additionally, bootstrap is in simple word the probability of which the result might be true. Bootstrap 27 would mean probability of 27 out of 100. There could be more complex explanation of this expression which you could find in the detailed text about it.
Actually the tree shows that all the LAUCA sequences are very similar to each other (some of them might be identical). In such case you should not wait highly supported inner clades. The clade of LAUCA itself however is highly supported. You can eliminate the long branch root, but the situation possibly will not change radically. You did not write which sequences were used, but seemingly these have no power enough to resolve the inner branching pattern. If you compare your sequences calculating e.g. p distance you would see how the individual sequences differ from each other. It is easily done in MEGA.
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