Sentence examples for using the ml methods from inspiring English sources

The hypothesis of positive selection was tested using the ML methods implemented in the CODEML program of PAML v4.2 [25], [25] and in the HyPhy software from the Datamonkey cluster [26].

Majority rule (50%) consensus trees were constructed using the Ml methods [ 33].

The effects of constraints using the ML methods will be illustrated by application to the E. coli K12 chromosome.

Majority rule (50%) consensus trees were constructed using the Ml methods [ 22] and the tree was viewed using TreeView [ 23].

It is worth noting that the Primate phylogenetic tree perfectly corresponds to that previously obtained by Makarenkov and Legendre [ 21], whereas the PheRS phylogeny was different from the tree obtained by Woese et al. [ 16] and Boc et al. [ 24], using the ML methods.

We found that the swine flu viruses are not clustered correctly by using the ML method with the J-C model (figure 4(a)) and the origin of A H1N1 virus is not clear by NJ method with Kimura model (figure 4(b)) since A H1N1 genomes are all very far away from other genomes.

In all cases phylogenetic trees were estimated using the ML method implemented by the PAUP* 4.0 package [73] and utilizing the best-fit model of nucleotide substitution as determined by MODELTEST [74], which in each case was the most general time-reversible GTR+Γ4+I model (full parameter values available from the authors on request).

Ancestral sequences were estimated using the ML method (MEGA).

In some cases, I reanalyzed published data sets using the ML method (see Materials and Methods).

The molecular clock for KN was tested using the ML method in MEGA.

Evolutionary history was inferred using the ML method, selecting topology with a superior log likelihood rate.