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Genetics/phylogenetic tree reliability


Dear Thanemozhi,

I'm a Chemical Engineer from the field water treatment. My group is just starting to work with molecular biology tools. We usually do sequencing after cloning but the number of clones is usually no more than 150. When we try to create phylogenetic trees with MegAlign (Dnastar)the reliability results obtained from bootstrap are quite low. What does it exactly mean? I know it's about the robustness of the structure... but I still don't know what does it mean. What could we do in future studies to improve these values?

Thank you very much for you time.



I am not an expert at phylogeny but from what I know: When sequences are highly similar and there is very little divergence- the program may not come with with a better bootstrap value. This indicates very little phylogenetic sub classes.
Also the distribution of variations in the homologous sequences can affect clustering of short branches giving rise to lower bootstrap values.

Bootstrap values are useful but do not prove anything for sure. Most criterions for judging trees are also based on predictions. Experts in this field suggest other criteria like neighbor joining, maximum likelihood, parsimony, etc

Try this site-phylodraw. in case you have not tried. It uses neighbor joining criteria.

If you can send me your email- I can provide the contact of an expert I know in this area who might be able to help you in depth.



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Thanemozhi Natarajan


Answers in Genetics, genomics, cytogenetics of syndromes, congenital anomalies, cancer, clinical genomics and interpretation of omics data.


More than 10 years. Doctoral research thesis on Congenital anomalies and cytogenetics, Recurrent reproductive failure and chromosomal abnormalities. Postdoctoral experience in Breast cancer research. Current: Clinical Genomics and Pharmacogenomics.


Cancer Cell International, Cancer Epidemiology Biomarkers and Prevention, Breast cancer research and treatment, Indian Journal of Pediatrics, BMC Proceedings, Pharmacogenetics and Genomics, Human Molecular Genetics, Frontiers in Genetics, Cancer Biomarkers.

PhD Biomedical Genetics

Awards and Honors
University Grants Commission Award for pursuing PhD level research (India); Travel awards to attend conferences.

Past/Present Clients
Post doctoral experience Cancer research, molecular epidemiology Current: Clininical Genomics and Pharmacogenomics

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