A phylogenetic tree was constructed by using a maximum likelihood algorithm as implemented by DNAML in PHYLIP (18 ).
After sequence alignment with ClustalW, a phylogenetic tree was constructed by using a maximum likelihood (ML) algorithm implemented in PAUP* (v. 4.0b10, Sinauer Associates, Inc., Sunderland, MA, USA).
Unrooted trees were then constructed by using a maximum likelihood estimation with a Jukes-Cantor model and γ-distributed rates, and by constructing 1,000 replicates to generate bootstrap support values.
A further refined system was then constructed by applying a maximum likelihood linear transform (MLLT) upon the LDA feature, which intended to reduce the correlation among feature dimensions so that the diagonal assumption of the Gaussians is satisfied.
Phylogenetic trees containing imported DENV viruses and others strains circulating throughout the world (from GenBank) were constructed by using a maximum likelihood model.
As a reference distribution in the KS test, a null distribution was constructed by a similar aggregation of maximum absolute fold changes, only with the association between scores and markers randomized for each target gene.
Fiber tract solutions were constructed by a streamline procedure, following directions of maximum diffusion at every point, and analyzed in an interactive visualization environment (TrackVis).
Phylogenetic trees based on pt genomes were constructed by Maximum-Likelihood (ML), Maximum Parsimony (MP) and Neighbor-Joining (NJ) methods using a dataset of 39 conserved proteins (7,406 amino-acid positions) encoded by the pt genomes of four taxa of red algae and 13 green-algal taxa (the green clade Viridiplantae as outgroup; Additional file 1: Figure S1A).
Thus, sequences contributing to extensive gaps in the conserved regions of the alignment were discarded and a phylogenetic tree constructed by the maximum likelihood PhyML method (see Additional file 2A).
