We have constructed a phylogenetic tree using 18 different ribosomal RNA gene sequences, Among them, 5 different sequences shown above 95% to 100% sequence similarity. But the bootstrap value shows less than 10.
We have used Neighbour Joining method to construct the tree in MEGA 7.
Thanks in advance.
I would recommend you to construct a Maximum Likelihood tree. Be careful about the meaning of bootstrap values between methods.
*Maybe you can try to construct it in http://www.atgc-montpellier.fr/phyml/
However... if you have a very high value of similarity between sequences, is very likely that the bootstrap values of a tree will be low. If you don't have a reasonable amount of differences between all of sequences (i.e. they are almost the same), there won't be enough signal to establish phylogenetic relations.
In a practical sense, when you see low bootstrap values in the intersection of two branches/leaves... that means that they are collapsing (considered the same lineage).
Thank U So much Sohali Keegan and Jose Alberto.
I tried using Maximum likelihood method, and it came out well..
As u mentioned about the Version, I also faced the difficulties in representing the tree.. And It got cleared now..
Thanks for your response.
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