Figure 7
Ancestral repeats: Comparison of all model parameters with and without splitting branches into multiple parts. Comparison of evolutionary model estimates, second-order root distribution estimates, branch length estimates and context-dependent model frequencies estimates between an underlying phylogenetic tree with and without branch partitioning. Colour coding for the evolutionary model parameters is identical to Figures 3,4 and 5. The second-order root distribution estimates are coloured as follows: π YX|A in black, π YX|C in red, π YX|G in green and π XY|T in yellow, with Y and X the two bases immediately preceding at the 5' side. The model frequencies are coloured as follows: π X|A|Y in black, πX|C|Yin red, πX|G|Yin green and πX|T|Yin yellow, with X the 5' and Y the 3' neighbouring base at the ancestral sequence of the branch (i.e. X, Y ∈ {A, C, G, T}).