Sentence examples for maximum likelihood programs from inspiring English sources

Aligned nucleotide and deduced amino acid sequences were analyzed by using the maximum parsimony, neighbor-joining, and maximum likelihood programs in the PAUP 4 package (26 ).

The Peters et al. pipeline takes full advantage of these developments, using RAxML, one of the fastest maximum likelihood programs available, for the final phylogenetic analysis.

Bayesian analysis was done using the program MrBayes [ 28, 29, 39], which deals with gaps just as other Maximum Likelihood programs [ 4, 42- 44].

Sequences were aligned by using the Clustal program in the MacVector (Oxford Molecular Group, Campbell, CA) software package, and phylogenetic analyses were conducted by using maximum parsimony, neighbor-joining, and maximum likelihood programs implemented in the PAUP 4.0 software (22 ).

The results were processed by a maximum likelihood program that determines full- and half-sibling groups based on genotypes [25].

Phylogenetic trees were calculated using a maximum likelihood program, RAxML [ 37], with a 100 bootstrap replicates.

The resulting multiple sequence alignment was used to infer the species phylogeny using the maximum likelihood program PhyML [ 43].

Phylogenetic trees were reconstructed with the PhyML program implemented in phylogeny.fr, using default parameters [ 38] or the Maximum Likelihood program [ 39] implemented in MEGA6 [ 40].

For the detection of positive selection, sites under diversifying selection were investigated with the maximum likelihood program CODEML of the PAML package [ 81].

A Perl script provided in the PhyloGenie package [ 83] was modified to use the fast maximum likelihood program PHYML version 2.4.4 [ 124].

A phylogenetic tree derived from the MUSCLE alignment was generated using the PROML (protein maximum likelihood) program from the Phylip package [ 34].