genomes with lower identity display closer relationship than genomes with higher identity, any idea why?
Hi all,
I have alignment five close-related genomes. A, B, C, D and E. A and B share nucleotide level identity as 96%, while between A and C this number is 94%. I used several methods to build their phylogeny trees. All the result showed A is closer to C and B. I am curious why. Shouldn't the genomes with higher similarity closer to each other?
Could anyone give me a hint?
Thank you so much!
Alexie.
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Yes, this is true but you are looking at percentage identity which is different from percentage similarity. Take a look at Sebastian's answer here . He also gives an example similar to your problem.