Fig. 3. A comparison of Read2Tree with a regular pipeline with assembly, orthology prediction and MSA computation.

a, A comparison of trees using the difference between the reference tree and either the tree of Read2Tree or the tree coming from the assembly approach. For dark blue, we had only Read2Tree trees as assemblies for these low coverages are not possible to obtain. Below zero (in dark or light blue), Read2Tree is more accurate, while above zero (in red), the assembly approach is more accurate and gray indicates no difference between the methodologies. b, A comparison of wall time needed from reads to availability of concatenated MSA showing the dependencies of available closest remaining reference and coverage.