PMC:1794230 / 11788-12673 JSONTXT

{"project":"2_test","denotations":[{"id":"17244358-9656490-1689311","span":{"begin":171,"end":173},"obj":"9656490"},{"id":"17244358-7463489-1689312","span":{"begin":246,"end":248},"obj":"7463489"},{"id":"17244358-15034147-1689313","span":{"begin":436,"end":438},"obj":"15034147"}],"text":"With each simulated gene, the sequences were generated respecting the phylogenetic tree shown in Figure 2, using the nucleotide evolution model of Halpern \u0026 Bruno (1998) [28] for transcription factor binding sites and the model of Kimura (1980) [29] (with a transition to transversion ratio of 3.0) for background positions, and without the introduction of sequence gaps. The phylogenetic tree was generated from aligned (using MUSCLE [30]) 16S rRNA gene data via PHYLIP [31] and tree branch lengths were scaled up by a factor of 13.5 so that the tree would represent evolution at neutral sequence positions rather than at the somewhat conserved 16S rRNA gene sequence positions. Although the factor of 13.5 reflects our previous experience (unpublished), it is not rigorously chosen; for this and other reasons, although this tree is realistic, it should not be considered definitive."}