Sentence examples for minimum evolution analyses from inspiring English sources
All minimum evolution analyses were performed using MEGA 2.1 [ 40] and PAUP [ 41], while likelihood and parsimony analyses, as well as the estimation of the specific gamma parameters for the minimum evolution analyses were carried out using PAUP.
The phylogenetic position of the 48 non-chimeric phylotypes from our samples was assessed by minimum evolution analyses.
Alternatively, the bootstrap method [ 51] was used with 10,000 replicates for minimum evolution analyses, as described above.
Minimum evolution analyses were performed using Kimura two-parameter distances with transversions-only, gamma corrected Kimura two-parameters distances with transversions-only, and paralinear distances.
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.
Statistical confidence in the deduced evolutionary trees was assessed by examining the Bayesian Posterior Probabilities (BPP) on the majority-rule consensus tree containing branch lengths for the Bayesian analyses or by bootstrapping the sequences for 1000 generations for the minimum evolution analyses.
Neighbor-joining (NJ) and minimum-evolution analyses were also performed in MEGA.
Finally, we performed minimum evolution (ME) analyses using 1000 bootstrap pseudorelicates in MEGA 5.05.
Minimum evolution (ME) analyses done with PHYLIP using the JTT + Γ model with global rearrangements and 10 rounds of random taxon addition (1 round was used in the bootstrap analysis).
Phylogenetic analyses with Poisson Model, including NJ, minimum evolution, and bootstrap analyses with 1000 replicates, were performed using MEGA 4.0 [4.0.
Neighbour-joining method, minimum evolution and UPMGA analyses were performed with the MEGA5 software package [ 44] using the uncorrected nucleotide differences (p-distance), which provides better results when examining a large number of sequences which contain a relatively small number of nucleotides [ 45].
