Sentence examples for using the gtrgamma model from inspiring English sources

Analyses were performed selecting the tree with the best log-likelihood out of a set of 1000 replicates, using the GTRGAMMA model of nucleotide substitution.

RAxML was run with 1,000 bootstrap replicates using the GTRGAMMA model.

The pruned alignment was used for phylogenetic reconstruction with RAxML using the GTRGAMMA model and 100 bootstrap pseudoreplicates.

Maximum likelihood analyses were conducted in RAxML [ 32] using the GTRGAMMA model for all genes to find the best tree.

Phylogenies were constructed with RAxML software version 7.2.6, using the GTRGAMMA model of sequence evolution with 100 bootstrap pseudoreplicates (Stamatakis and Alachiotis 2010).

An ML phylogeny was generated using RAxML version 7.2.6, using the GTRGAMMA model of sequence evolution with 100 bootstrap pseudoreplicates (Stamatakis and Alachiotis 2010).

We used the GTRGAMMA model, which includes a parameter for rate heterogeneity among sites and chose not to include a parameter for estimating the proportion of invariable sites [ 125, 126].

First, we obtained the best estimate of phylogeny by analysing all the data using the GTRGAMMA algorithm implementing the GTR+Γ model with 25 discrete rate categories.

Individual gene trees are inferred using RAxML with the GTRGAMMA model, and then a species tree is recovered from those gene trees using ASTRAL.

Finally, ML phylogenies under the best partitioning schemes were estimated using the GTRGAMMA algorithm and bootstrap support (1000 pseudoreplicates) was calculated for these topologies using the rapid algorithm implementing the GTRCAT routine (Stamatakis, 2006 a ; Stamatakis, Hoover & Rougemont, 2008).

We used the GTRGAMMA substitution model suggested by jModelTest 2.1.4 [ 84, 85].