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These analyses implement FASTA and BLAST comparisons against non-redundant databases as well as GO annotation.
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This approach is evolving towards more powerful physically based analyses implemented in advanced computational models.
The system under investigation was analyzed by means of full dynamic time history analyses, implementing rigorous finite element models.
Maximum likelihood and Bayesian analyses implemented an optimal model of DNA sequence evolution determined using Modeltest 3.7 [76].
Bayesian inference and maximum likelihood analyses implemented a GTR+G model of DNA sequence evolution, the most appropriate model as determined by the Akaike Information Criterion in Modeltest.
All analyses implemented the GTR+G+I model of DNA substitution, which received the best Akaike information score by Modeltest 3.06 [32].
Phylogenetic analyses implementing both maximum likelihood and parsimony of the 731 representative core rickettsial proteins (discussed below) resulted in robust estimates for these 10 taxa (Figure 3).
The analyses implemented in JMATING focus on mating frequency data.
Relationships among copies were inferred from exon sequences using Bayesian Markov Chain Monte Carlo (MCMC) analyses implemented in p4 (v0.88.r221; [ 34]).
The normalized intensity data were log2 transformed for subsequent analyses implemented using R-bioconductor (v 2.10.0).
The nucleotide sequences of both MAT idiomorphs were compared using dotplot (matrix) analyses implemented in Geneious.
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