Sentence examples for using the bionj tree from inspiring English sources

We used a general time-reversible rate matrix (GTR) with six substitution categories estimated from the alignment using the BioNJ tree.

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

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

To test the consistency and robustness of tree topologies, consensus trees were generated from 1000 bootstrap replicates using the BioNJ algorithm [ 25] and the JTT model of amino acid substitution.

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

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].

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 same topology was retrieved when using two different starting trees: the Bionj Tree or the best topology found using the DNA alignment.

Finally, for ML analyses, the BioNJ tree was used to start the iterative searches and the Blosum62 matrix was chosen to model amino acidic substitutions.