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Phylogenetic trees were then computed by maximum likelihood (Figure 4) and Bayesian analysis (Figure 5).

A phylogenetic tree of the 481 hemagglutinin sequences was constructed via gamma-corrected, general time-reversible maximum likelihood (Figure S1).

Phylogenetic analyses place this gene family either within the NKL subclass (maximum likelihood; Figure 1) or close to the division between the NKL and HOXL subclasses (neighbor-joining; Additional file 3).

This result was reproducible with different phylogenetic analysis algorithms (neighbor joining, maximum parsimony, maximum likelihood; Figure S1 in Additional file 1), suggesting a European genotype for C. ulcerans which is different from the genotypes described from South America [ 34] and Asia [ 24].

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neighbor-joining (Figure 1), maximum-likelihood (Figure S13) and Bayesian analysis (Figure S14).

Use of other amino acid alignment methods (data not shown) and different methods of phylogenetic reconstruction, such as maximum-likelihood (Figure S11) or Bayesian analysis (Figure S12), did not alter the branching of the C. intestinalis DIA1 gene to that consistent with the current evolutionary model of species.

All of the organisms with protosteloid types of fruiting group within Amoebozoa in our maximum likelihood tree (Figure 3).

Subsequently, a sample of 87 KLK protein sequences was chosen for more accurate phylogenetic analysis using the maximum likelihood method (Figure 3).

The STE11 gene in F. depauperata does not appear to be mating type specific by either Parsimony or Maximum Likelihood analyses (Figure 10).

The phylogenetic result obtained by using maximum likelihood method (figure 4(a)) showed that the swine flu virus genomes were not clustered correctly.

Representative full-length H6 HA sequences from each of the 4 different lineages were used to construct a bootstrapped DNA maximum likelihood tree (Figure 2).

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