Sentence examples for based on gene tree from inspiring English sources
Since the gene tree was different from the species tree, analyses were done based on gene tree as well as the species tree.
Figure 3 shows a heat map of the data matrix with data organized based on gene tree and condition tree clusters.
A different approach, based on gene tree comparisons, showed that with the exception of species monophyly, there was virtually no consensus history between genes (supplementary fig. S7, Supplementary Material online).
Existing methods for inferring species trees from collections of gene trees can be divided into two broad categories: non-parametric methods based on gene tree parsimony (GTP), and parametric methods that use likelihood (e.g., [ 7, 8]) or Bayesian frameworks (e.g., [ 9- 11]).
Tests of positive selection were performed using the codeml program in the package PAML 3.15 [49] based on gene trees of members of the Culicidae.
Instead we need statistical tools rather than majority rule heuristics for inferring the species tree based on gene trees.
The Berkeley PhyloFacts Orthology Group (PHOG) [ 55] algorithm makes use of both tree topology and tree edge lengths to identify orthologs based on gene trees in the PhyloFacts Phylogenomic Encyclopedia [ 11]; a tree-distance threshold allows biologists control over the precision recall trade-off and to target specific taxonomic distances.
In a study based on gene trees instead of species trees, Forslund et al. (2008) argued that even between 5.6% and 12.4% of domain architecture could have originated several times independently, although approximately two-third of the cases involve only the loss of domains.
Here, we identified potential HGT events based on gene-tree species-tree reconciliation.
Gene conversion events can lead to errors in the phylogenetic reconstructions of gene trees and, therefore, may bias gene BD rate estimates based on gene tree species tree (GT-ST) reconciliation.
New and complicated evolutionary models based only on gene tree conflicts should not be advanced without explicit experimental attempts to falsify them.
