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(K) Maximum likelihood phylogenies of the PA gene of the new H7N9 isolates.
Figure 6 Maximum likelihood phylogenies of A. ITS (left) and B. trnL-F intron spacer region (right) with clade supports (LB: upper; PB: lower).
To assess nodal support on maximum likelihood phylogenies, we report approximate Likelihood Ratio Test (aLRT) scores.
Maximum likelihood phylogenies were evaluated for evidence of compartmentalization using four statistical tests.
While bootstrap values were improved in maximum likelihood phylogenies considering only Chlorobi sequences, this was not true of Bacteroidetes CrtB, CrtI and CrtZ trees (data not shown).
Maximum likelihood phylogenies with the same sequence datasets were also estimated using PhyML 3.0, providing similar tree topologies (data not shown).
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FastTree 2 allows the inference of maximum-likelihood phylogenies for huge alignments.
These character states were then mapped onto neighbor-joining, Bayesian, and maximum-likelihood phylogenies of the 14 Nematostella genes.
Maximum-likelihood phylogenies were constructed using (i) PhyML (23) and (ii) RAxML (Linux version 7.2.8) (24).
The maximum-likelihood phylogenies were inferred using PhyML v3.0 (Guindon and Gascuel 2003).
Additional file 6: Maximum-likelihood phylogenies based on whole genome and SNP concatenated sequence alignment.
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