Sentence examples for maximum likelihood matrices from inspiring English sources
In order to exclude redundant species, we used PUZZLE to establish maximum likelihood matrices for the 469 alignments, taking into account among-site rate variation [ 14, 23].
To evaluate the degree of distinction among the rep genes and intergenic region of the different incompatibility groups, we determined maximum likelihood matrices and then calculated the average distance over all possible pairs of sequences (see Methods).
Finally, maximum likelihood distance matrices were inferred using the model specifications from jModelTest; this was done with PUZZLE [ 22].
We calculated maximum likelihood distance matrix, using DNA sequence from six nuclear loci, to represent phylogenetic differences among taxa.
A maximum likelihood distance matrix was built by Tree-puzzle 5.2 (Schmidt et al. 2002) under the Hasegawa Kishino Yano + Γ model.
Neighbor-Joining (NJ) trees were calculated by the NEIGHBOR program of the PHYLIP package [ 25], using Maximum Likelihood (ML) distance matrices (JTT model including a Γ-correction) computed by TREE-PUZZLE 5.1 [ 26].
The analyses with single-matrix models used amino acid frequencies inferred from the data by maximum likelihood; both single-matrix and site-heterogeneous analyses employed a discrete approximation to the gamma distribution with four rate categories (Yang 1994) for modeling across-site rate variation.
We also concatenated a matrix with 10%% of the most slowly evolving genes for a partitioned maximum likelihood analysis ('Slow108' matrix).
Considering EU, AS and CIQ as possible sources of colonization of OZ, we developed eleven phylogeographic hypotheses, based on historical possibilities, each of which had a corresponding maximum likelihood migration rate matrix (Additional file 1: Table S2, Additional 4: Figure S3).
Using three data matrices, maximum likelihood (ML) phylogenetic analyses were conducted using 79 protein-coding genes from 56 orders of seed plants.
For all matrices, Maximum likelihood (ML) analyses were performed with the Pthreads-parallelized version of RAxML 7.2.8 (Stamatakis 2006; Ott et al. 2007) under a rapid bootstrap analysis (-f a) applying the PROTCATWAGF model.
