Which DNA sequences should i select in phylogenetic analysis as i am getting very low bootstrap value for phylogenetic tree using ML method?

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Patrice Showers Corneli

This depends entirely on what organisms you are studying and how deep the divergence time is. Sounds like for your problem, the sequences you are using are not sufficiently variable.

Abdul Waheed Khan

I am using fragment of Hepatitis C virus ns5b gene

How long are the sequences?

Dear Patrice, its about 272 bp long sequence