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. 2014 Sep 29;9(9):e107389. doi: 10.1371/journal.pone.0107389

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© 2014 Aiamkitsumrit et al

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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A total of nine regions of LTR were chosen based on the known functions. Utilizing a maximum-likelihood algorithm, phylogenetic trees were created based upon a total of 18 sequences, which included nine sequences of X4 and nine sequences of R5. A simple Python script was generated to automate the process of creating the hundreds of trees; additionally, each branch distance was calculated between all pairs of X4 and R5 sequences. Each group of distances was tested for significant differences using a two-tailed student t-test [115]. The MGD, SD, and P value of each group are shown. The three most significant comparisons are shown in green and the three least significant ones in purple.