The second way of relating gene trees to species trees is to think of the gene trees as contained "within" the species tree.
4, 6 Using an average linkage hierarchical clustering algorithm with a Euclidean distance metric, in which genes are iteratively grouped together based on their distance metric, we determined that COX-2, Plk3, FAS, TP53INP1 and TP53INP11 are contained within the same sub-tree structure (Suppl. Fig. 4), thereby implicating co-regulation among these genes upon T/C-28a2 cell exposure to fluid shear.
Once we enumerate the trees contained within the estimated networks, or within the set of trees estimated by the traditional phylogenetic approaches, we need to compare these trees to the model tree(s).
On a general level, larger proportions of nutrients are contained within the bark of smaller trees.
Where elBulli is old-fashioned and even a little run-down, as though to frame the hyper-modernity of its plates all the more sharply, El Celler de Can Roca, to give the full name of the Roca brothers' three-star place, is of exquisitely contemporary design, with small groves of poplar trees contained within the zigzagged green-glass walls of the restaurant proper.
First, we built a neighbor-joining tree for each of the thirty 1-Mb segments based on only the information contained within the segment, and then we performed the panel-selection algorithms on the tree.
The method works by examining each internal branch of each input tree, and assigning a '1' to any taxa contained within the clade defined by that internal branch.
Also, we constructed the phylogenetic trees based on the HesA and Orf1 sequences which are contained within the complete nif gene cluster.
The football world was almost fully contained within the game.
Both of these visions are now contained within the Democratic Party.
No such provision was contained within the EU referendum legislation.
