Sentence examples for using the bionj algorithm from inspiring English sources

The distance matrix was then used to calculate a phylogenetic tree using the BIONJ algorithm [24] and a neighbornet network [25] (Figures 3 & S2).

NJ analyses were done using the BioNJ algorithm [ 70] and 1000 bootstrap replicates.

NJ analyses were done using the BioNJ algorithm [ 67] and 10,000 bootstrap replicates.

Neighbor-joining analyses were done using the BioNJ algorithm [ 70] and 1000 bootstrap replicates on MEGA version 4.0 [ 71].

The obtained values are subsequently clustered using the BioNJ algorithm [ 68], leading to a classification tree containing 472 proteins.

Neighbour-joining (NJ) reconstructions were performed with the PAUP 4.0 program using the BioNJ algorithm and 10,000 bootstrap replicates [ 52, 53].

In principle, any method to estimate a starting tree could be used since it has been argued that a non-random tree is likely to be sufficient for model selection [ 59- 61]; in our implementation, we use the BioNJ algorithm implemented in PhyML [ 24] to estimate a neighbor joining starting tree, then re-optimize the branch lengths of this tree in PhyML using the GTR + I + G model.

The tree was generated with the APE package (version 3.0-11) foR R (version 3.0.2) using the bionj function which uses the minimum evolution algorithm of Desper and Gascuel [ 121].

This method (termed BIONJ-GTR) used the BIONJ reconstruction algorithm [ 43] on distances obtained under the general time-reversible model with invariant sites and Gamma distribution of rates across variant sites (GTR+ Γ +I) [ 8, 44].

Trees were then built using the BioNJ (Kimura correction), Parsimony and Maximum likelyhood methods as implemented in SeaView.

NJ trees using the BIONJ method [ 42, 44], MP trees and ML trees were reconstructed by PAUP*4.0b10 [ 28].