My phylogenetic tree topology is fine but the confidence (nodes bootstrap value) is quite less than the threshold. Do journals accepts such trees?

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Daniel Poppleton

It can be fine. It depends on the alternative topologies that the bootstrap trees give. Alternatively a different method can help, baysian for instance, as this may improve your support values.

Aditya Gupta

Yes suellen. Sometime it happens. Try to go for some alternate trees along with BEC and evolutionary divergence for the species.