Sentence examples for using the bionj function from inspiring English sources

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.

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

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

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].

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

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

We used pairwise LCNS−1 values, with a frog (Xenopus tropicalis) as the outgroup, to construct both topology-constrained and topology-unconstrained phylogenies using the BioNJ method in PAUP (Swofford 2003).

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.