Sentence examples for model discrete gamma from inspiring English sources

A preliminary maximum-likelihood tree was constructed using the FastTree program with default parameters (JTT evolutionary model, discrete gamma model with 20 rate categories [ 19]) [ 19].

A preliminary tree was constructed using the FastTree program with default parameters (JTT evolutionary model, discrete gamma model with 20 rate categories) [ 33].

Phylogenetic analysis was performed using the FastTree program with default parameters (JTT evolutionary model, discrete gamma model with 20 rate categories) [ 27].

A tree constructed using the FastTree program [ 69] with default parameters (JTT evolutionary model, discrete gamma model with 20 rate categories was used to reconstruct a preliminary maximum-likelihood (ML) tree.

The resulting 160-column alignment was used to construct a maximum likelihood phylogenetic tree using the FastTree program with default parameters (JTT evolutionary model, discrete gamma model with 20 rate categories) [ 31].

The resulting 278-column alignment was used to construct two maximum likelihood (ML) phylogenetic trees, one using the FastTree program [ 36] with default parameters (JTT evolutionary model, discrete gamma model with 20 rate categories) and the other using the MOLPHY program [ 37] with the JTT substitution matrix to perform local rearrangement of an original Fitch tree [ 38].

Phylogenetic analysis was performed using PhyML with the RtREV model, a discrete gamma model with 10 categories and estimated gamma shape parameter, best of the NNIs and SPRs tree topology search; statistical support was approximated by aLRT-SH values [ 27].

A maximum likelihood tree with 100 bootstrap replicates was constructed with the PHYML program [ 63] using the JTT amino acid substitution model, a discrete gamma model with four categories and an estimated shape parameter of 1.385.

NJ trees were calculated with Phylo_Win (version 2.0) using a Poisson correction and pairwise gap removal (Galtier et al. 1996), whereas ML trees were obtained with PhyML (version 2.4.4) using a Jones, Taylor, and Thornton model, a discrete gamma model with four categories, a gamma shape parameter of two and a ML estimate of the proportion of invariable sites (Guindon and Gascuel 2003).

The phylogeny of the aaxA, aaxB and aaxC genes was inferred using the PhyML program (ver. 3.0.1) [ 54], with the HKY85 nucleotide substitution model, a discrete gamma model with 4 categories of sites and estimated transition/transversion ratios of 3.9 (aaxA), 4.8 (aaxC) and 6.1 (aaxB).

The best fitting nucleotide substitution model for the phylogenetic alignments was inferred to be the Hasegawa Kishino Yano model with discrete gamma and invariant among-site rate variation.