Sliding MinPD

Building evolutionary networks of serial samples via a recombination detection approach

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Supplementary Material: Patient 8 ML Tree

A Maximum Likelihood (ML) tree of Shankarappa's [1] patient 8 produced by fastDNAml 1.2.2 (HKY85 model, Ts/Tv of 2, and empirical base frequencies) is shown below.

Figure 2. ML tree of patient 8. Sequences with the X4 mutation are marked with an x. Prefix of IDs indicates sampling time. GenBank ID of p8c081-14 is shortened to 81-14 and refers to sequence 14 from sampling time 81 months of patient 8. 

References

[1] Shankarappa, R., Margolick, R. B., Gange, S. J., Upchurch, D., Farzadegan, H., Gupta, P., Rinaldo, C. R., Learn, G. H., He, X., Huang, X.-L., and Mullins, J. I. (1999). Consistent viral evolutionary changes associated with the progression of HIV-1 infection. J. Virol. 73:10489-10502.