Sentence examples for using the ml tree from inspiring English sources

The robustness of our results to the tree topology is examined later, by duplicating the analysis using the ML tree under the GTR+G model (PhyML) [21].

Using the ML tree obtained from the combined molecular dataset as a topological constraint, we compared the branch lengths estimated from the three different morphological datasets (17 continuous, 11 meristic, and 28 continuous+meristic characters) used in the first PCA.

Using the ML tree as the backbone tree, alternative trees were produced by switching branches using Treeview (version 1.6.6).

Using the ML tree topologies generated above for each gene, dSbranch lengths were estimated in HyPhy version 0.99 for UNIX [ 43] using the MG94W9 codon model [ 15] and allowing for independent dN and dS values for each branch (the local parameters option).

To test alternative hypotheses to the Archaeplastida monophyly, we manually generated 31 competing phylogenetic trees (supplementary fig. S4, Supplementary Material online) with MacClade v4.08a (http://macclade.org/index.html, last accessed October 9, 2014), using the ML tree generated from the protein alignment as a reference.

Since the phylogenetic organizations of the three trees are identical, we only used the ML tree for illustration.

We used the ML tree as a starting tree, but introduced random perturbations into it to enable detection of possible convergence problems (using the command "mcmcp nperts = 5").

We used the ML tree generated with RaxML under the constraint that sFRP and/or netrin were monophyletic (model WAG + Γ 8) + I) as the null hypothesis topology T0 (list of tested hypothesis in table 2).

To analyse evolution of life form, chromosome number, and stylar morphology, we used the ML tree built from the condensed dataset for the 262 species (Additional file 12: Figure S10).

In Brassica, the analysis of ten trees randomly chosen from the 93 credible set consistently recovered 11 of the twelve sites identified by the BEB procedure using the ML-tree.

For the latter groups branch lengths were calculated using the ML consensus tree as a user defined tree in TreePuzzle [ 74].