Neighbor joining bootstrap consensus tree (K2P distances) for nucleotide sequences recovered at 5 time points for patient ALL-30 (samples ALL-30-01 through ALL-30-05 in Table 3). The patient was initially enrolled in a clinical study testing the use of nilotinib and imatinib administered in rotation in 6-week cycles. Sample ALL-30-01 (time point 1) was collected after the first (nilotinib) cycle. Sample ALL-30-02 (time point 2) was collected after the second (imatinib) cycle. Sample ALL-30-03 (time point 3) was collected after the fourth cycle. Sample ALL-30-04 was collected after the patient had discontinued the nilotinib-imatinib rotation schedule for hematologic relapse and had received 2 weeks of dasatinib treatment. Sample ALL-30-05 was collected after 6 weeks of dasatinib treatment and a few days before the exitus. Branches with <25% support are collapsed to polytomies. Amino acid substitutions are mapped onto the tree and shown for each sequence along with the percentage of reads that each sequence represented at each time point. “Germline” indicates the unmutated sequence. The scale bar shows substitutions per site. The colors identify the 3 sequence clusters that can be recognized (A-C; see “Further insights into BCR-ABL KD sequence evolution: a phylogenetic approach” for details).