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The 'essential' core recovered the reference tree in all 60-genes concatenates generated, whereas the 'universal' core with 60 genes concatenated only yielded a null Robinson-Foulds (RF) distance to the reference tree in 41 of the 100 concatenates.
To assess the fidelity with which individual genes recovered the reference tree on a holistic scale, we calculated the topological distance between each individual gene tree and the concatenated tree using the Symmetric Difference [ 30] computed by the TreeDist program included in the Phylip v3.68 package [ 31].
The final value obtained for the 60-genes concatenates reflected this clear discrepancy: concatenates for the 'essential' core had RF distances of zero, since all of them recovered the reference tree, while the average distance of 60-genes concatenates from the 'universal' core was 5.78.
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Suppose data is from a generative model with infinite sample size, will L1 minimization framework be able to recover the reference dictionary?
The results show that we are able to recover the reference Gauss coefficients used to build the synthetic data set with a very good accuracy.
Finally, we analyzed the performance of the individual gene trees in the different data sets for recovering the reference tree topology.
In our study, the mt tRNA genes showed the lowest performance, whereas in Mueller [ 27] these genes demonstrated a medium ability to recover the reference topology.
The best performing approach is a novel hybrid strategy, which combines a random walk-based reduction of the graph with a shortest paths-based algorithm, and which recovers the reference pathways with an accuracy of ∼77%.
Regarding whole coding sequence alignments, the inferred relative positioning of the lineages was in agreement with the reference species tree only for Cytb, ND1 and ND6 gene trees, while the concatenated "supergene" did not recover the reference species topology (Additional file 12).
Moreover, results of phylogenetic performance indicated that none of the individual mt genes recovered the whole-genome reference ML tree, which may indicate that larger data sets may provide more informative sites for this particular phylogenetic question.
The turbine blade temperature and the compressor surge margin could be recovered to the reference values by either under-firing or compressor air bleeding, which are effective for blade temperature control and surge margin control, respectively.
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