Sentence examples for minimum evolution algorithm from inspiring English sources
The Minimum evolution algorithm was applied based on the Nucleotide Maximum Composite Likelihood analysis of all positions.
We also used the Minimum Evolution algorithm [40], Log(Det) distances [41] and the Kimura 2 correction parameter [42].
The resulting distance matrices were then used to construct distance trees using FastME with the initial tree construction option of the Greedy Minimum Evolution algorithm and the tree swapping option of the Balanced Nearest Neighbor Interchanges algorithm.
Subsequently, a phylogenetic tree was constructed with the Minimum Evolution algorithm by using MEGA6 [ 59].
A consensus phylogeny using the minimum evolution algorithm resolves two major clusters of strains (supplementary fig. S4, Supplementary Material online).
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].
We used maximum parsimony, neighbor-joining, or minimum evolution algorithms with 2,000 replicates for bootstrap support of tree groupings.
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.
Phylogenetic analysis was performed with the protein sequences of the here investigated genes and sequences taken from PeroxiBase using neighborhood joining (Fig. 14B), maximum parsimony and minimum evolution algorithms (Additional files 9 and 10).
Alignment with phylogenetic tree construction by neighbor-joining, maximum-parsimony, or minimum-evolution algorithms was also performed for the NS5 region of all available flaviviruses because extensive sequencing and phylogenetic analysis have been conducted for this region (16 ).
A dendrogram constructed on the basis of the Minimum Evolution clustering algorithm revealed that Pistacia vera has closer relationships with P. khinjuk, than with Pistacia integerrima, Pistacia palaestina, Pistacia atlantica and Pistacia mutica.
