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The most frequent tree species are listed in Table 1.
The abundance of aspen in our stands is comparable to the abundance of birch in Finland which constitutes 17% of growing stock and is the third most frequent tree species of the country (Metsätilastollinen vuosikirja 2013).
The density tree of the most frequent tree and the ML gene trees that significantly differed from the most frequent tree are shown in Additional file 1: Figure S1.
When most trees agree in topology and branch lengths, the most frequent tree topology, properly annotated, can give a fair representation of the posterior distribution.
However, consistent with previous results, the most frequent tree topology for Z-linked genes was that linking P. appalachiensis and P. canadensis (table 2) while the most frequent tree topology for mitochondrial genes was that linking P. appalachiensis and P. glaucus (table 3).
Likewise, the Densitree [ 62] depicting the posterior distribution of the 25,000 trees as inferred from the Bayesian divergence age analysis in BEAST suggests the most frequent tree topology to be identical to that obtained from ML and Bayesian analyses.
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Here, we present the Newick utilities, a set of automatable filters that implement the most frequent tree-processing operations.
When N = 3, (8) becomes (5) and the MP-EST tree is the most frequent gene tree triple with an internal branch of length described in (6).
If the gene's ML tree was not significantly different than the most frequent ML tree, then the latter was used as the representative tree for that gene for the frequency calculations of tree node support.
Furthermore, given any set of gene trees in which the most frequent quartet tree is unique for all four taxa and equal to the species tree on the four taxa, the true species tree T* will have the unique maximum quartet support score.
For each gene, we tested whether its ML tree was significantly different than the most frequent ML tree.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com