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!