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The results show that NJ has difficulties in the Felsenstein zone where the long-branch attraction problem is present (that is, small a and large b) and ML fails for largely divergent trees (note that trees here have at most 2.25 pairwise divergence, whereas similar studies have even used divergences of about 7.0 expected substitutions per site [ 18]).
Specially for largely divergent trees, we observe that EMtree gives the best results and is less subject to long-branch attraction.
Summing up, an EM approach on Markov models provides an accurate 4-taxon tree reconstruction method suited for data not known to satisfy homogeneity and very useful as input of quartet-based methods, specially for largely divergent trees.
The method presented in this paper is well suited for reconstructing the topology of any number of taxa via quartet-based methods and is highly accurate, specially regarding largely divergent trees and time nonhomogeneous data.
A detailed look at these figures reveals that for largely divergent trees (that is, b=0.1, the last bar in each plot), EMtree is the best quartet input method among those considered here, as its results outperform NJ and ML for both QuartetSuite and QFIT and in all tree topologies.
In these tables we observe that QuartetSuite gives the lowest distance to the original tree in general and that the best results for largely divergent trees (b = 0.1) are obtained by EMtree (for both QuartetSuite and QFIT and all tree topologies).
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Climate matching necessarily requires introduction of phenotypically divergent tree populations.
In this way, we could identify the common expressed CAZyme repertoires involved in carbohydrate metabolism in wood-forming tissues of two evolutionary divergent tree genera.
The conservation of these expression investment patterns between source (mature leaves) and sink (immature xylem) tissues of divergent tree species indicates a conserved mechanism for CW biosynthesis at the functional domain level, and highlights the importance of regulation of these genes at the level of transcript abundance.
The pure species genetic map for E. camaldulensis was developed with RAPDs, RFLPs and SSRs by selecting highly divergent parent trees for mapping population generation (Agrama et al. [2002]).
The divergent gene trees for DDX19A/B and TUBG1/2 show monophyletic clades in which all the eutherian mammal orthologues cluster.
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