Sentence examples for multiple optimal trees from inspiring English sources

First, efficient heuristics use the root information, and second, the search does not continue to find multiple optimal trees.

However, if multiple optimal trees were presented, and the authors explicitly preferred one or a subset of these, we followed this preference [ 32].

In the case of maximum parsimony, multiple optimal trees are usually generated for each replicate (note that multiple trees are possible with ML, although in practice they are not typically recovered).

A possible explanation for the long computation times observed in these groups is that there was not enough time for selection to get rid of mildly deleterious mutations (in the case of codeml models) or that multiple optimal solutions for tree topology are available (in the case phylogenetic tree reconstruction).

In the analysis reported here, 20% of 1128 cyanobacterial trees had multiple optimal solutions with inconsistent event histories.

If a tree had multiple optimal solutions (one or more optimal roots or reconciliations for a specified root), it was only retained if all solutions yielded the same counts for each event.

The integration of alignment and tree searching into a single procedure to produce globally optimal trees allows for evaluating multiple unique homology schemes on a consistent theoretical basis, as both are evaluated using the same criteria [ 39, 40].

Using NOTUNG (Stolzer et al., 2012), we repeated their analysis using only transfer loss (TL) and transfer loss-ILS models of reconciliation (with default event costs) applied to TreeFix-TL gene trees, and we find that temporal infeasibility and conflicting multiple optimal solutions affect only 0.6% and 0 0.4% of gene trees, far fewer than the ∼10 and ∼20% previously reported.

Even though multiple optimal solutions are not uncommon in phylogenetics (e.g. there can be several most parsimonious trees [ 26]), it could still be of interest to develop ways to systematically select specific optimal trees.

Experimentation with these settings revealed that default options were sufficient for finding optimal trees.

Multiple optimal configurations are shown to exist.