Sentence examples for minimum evolution model from inspiring English sources

All trees presented here were built using a minimum evolution model and bootstrapped one thousand times.

Other methods (including UPGMA and minimum evolution) and models (including p-distance, number of differences and Tajima-Nei models) of phylogenetic reconstruction resulted in differences in arrangement only within the highly similar Class B Mup genes.

In this study, a methodology involving a Domino Evolution Graph (DEG) model and a Minimum Evolution Time (MET) algorithm is proposed to model the spatial-temporal evolution of domino accidents.

Bootstrapping (500 replicates) was carried out using MEGA (version 3.1) [ 61] or the Phylip group of programs (version 3.5) [ 62] using neighbor-joining or minimum evolution methods and several models of amino acid substitution, including poisson correction and Jones, Taylor & Thornton (JTT).

These concatenated datasets were analyzed using maximum likelihood (JTT + gamma model, quartet puzzling with 1000 steps) [ 38], minimum evolution (Neighbor-joining, Poisson + gamma model, 2000 bootstraps, complete deletion) [ 37], and Bayesian Inference (JTT + gamma model, 50,000 generations, 4 chains with starting temp = 0.2) [ 39].

PAUP* [ 47] was used for minimum evolution analyses using the GTR model of substitution [ 48, 49], and taking into account a gamma-shaped distribution of the rates of substitution among sites, with eight rate categories.

Minimum evolution trees were constructed from models of substitution specified by Modeltest, with starting trees obtained by neighbor joining followed by application of a tree-bisection-reconnection (TBR) branch-swapping algorithm during a heuristic search for the optimal tree.

For example, some procedures include methods of branch length estimation that are known to yield underestimates such as parsimony or minimum evolution methods [ 27], maximum likelihood models that neglect between-site rate heterogeneity [ 28], or use Bayesian methods with strong prior assumptions biased towards producing young date estimates and fast early molecular rates [ 26, 29, 30].

Additional trees were built, using alternate phylogenetic methods (neighbour-joining trees under various models of evolution, minimum evolution trees and maximum parsimony trees) to verify the observed phylogeny.

For the two PDGFRβ analyses, the phylogenetic relationships among sequences were estimated using minimum evolution with the Jones-Taylor-Thorten [30] model of protein evolution with gamma-distributed rates, and 1,000 bootstrap replications.

Phylogenetic analyses on RanGAP2 sequences were carried out using, maximum likelihood and maximum parsimony methods and minimum evolution algorithms with the Tamura 3-parameter model [ 52] and a Gamma parameter of 0.163.