Sentence examples for maximum gene tree from inspiring English sources

In this case we can rule out AGTs when we consider the maximum gene tree support that an AGT can have is less than 33%.

Maximum likelihood gene tree of TLR4.

These sequences were aligned with PASTA2 and we then constructed a maximum likelihood gene tree with RAxML3, performing 100 bootstrap replicates41,42 (Extended Data Fig. 7).

We also constructed a maximum likelihood gene tree with PHYLIP's dnaml [84] and obtained the same topology.

We then estimated a maximum likelihood gene tree for each locus using PHYML [ 48] using the appropriate model selected by MrAIC.

A distance matrix (Additional file 1) was generated for each maximum likelihood gene tree, showing the relative branch lengths between each organism for each particular protein.

The maximum likelihood gene tree for each set of orthologs was reconstructed using PhyML with the following parameters: Model of amino acids substitution = WAG, discrete gamma model, number of categories = 4, tree topology search = NNIs, and optimizing over all other parameters (tlr, proportion of invariant sites estimated from the data).

We evaluated model fit by comparing nDC for the 'best' cyt b maximum-likelihood gene tree to that from the simulated gene trees (treated as rooted).

From theses alignments we inferred the maximum likelihood gene trees, which were subsequently used to reconstruct the species' phylogeny.

Hence, we aligned the homologs resulting from the BLAST search for the 579 Blochmannia genes and obtained the corresponding maximum likelihood gene trees.

Maximum likelihood gene trees were then assembled using the phylogenetic software Phyml [ 93] and the best model of amino acid substitution according to the ProtTest results (Additional file 2).