when I am doing phlyogenetic analysis after gene seuqencing of my bacteria, I very often obtain a tree like this (rpoB gene):
Here, what I understood is that the samples make a cluster in 99% of the cases and thus belong to the same species.
The bootstrap value (500 replicates) at the node of the samples and the closest relative is only 60. Sometimes, it is even less for other trees. I am not sure about how to interprete this value.
I think it means that in 60% of the calculations the tree bifurcates into two branches giving rise to the shown topology.
I am note sure what the remaining 40% could look like. Could it have more than two branches or could the samples and species 24 fall into one cluster?
What does it mean and what can I infer from such a tree?
(The highest similarity in Blast search normally is <90% for rpoB.
Additionally, I will do biochemical tests and a DNA fingerprint using the samples and the closest relatives regarding the blast search.)
Thanks a lot!
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Interpretation of bootstrap values of my tree
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