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Consequently, modeling and phylogenetic analysis strongly suggest that LAP1 and TorsinA might form a heterohexameric ring with three active sites in which TorsinA and its partner subunits alternate to form the ring.
According to homology modeling and phylogenetic analysis, the NIP subfamily can be further divided into three subgroups with distinct biological functions (NIP I, NIP II, and NIP III).
In the past few years, microRNAs have gained attention as alternative sequence markers for evolutionary modeling and phylogenetic analysis (Sempere et al. 2006, 2007; Wheeler et al. 2009; Rota-Stabelli et al. 2011).
Overall however, based on PCA, ecological niche modeling and phylogenetic signal analyses, our results do provide some support to the idea that in terms of diversification, ecological speciation as viewed through climate has not played a major role in the evolution of Isolona and Monodora species.
On the other hand, differently from what is predicted in databases, according molecular modeling and phylogenetic analysis, X. citri does not show a proper taurine transporter, but two different ABC systems related to the alkanesulfonate/sulfonate transport that were recently acquired during evolution.
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Phylogenetic diversity was assessed by means of two indices, phylogenetic diversity (PD) and phylogenetic diversity-rate (PD-rate).
For each group, sequence alignments and phylogenetic trees were built.
and F. asiaticum, respectively, by PCR RFLP and phylogenetic analysis.
MSA and phylogenetic tree.
The former has concentrated on either explicitly modeling substitution, insertion, and deletion through variants of the TKF model (Thorne et al. 1991, 1992; Redelings and Suchard 2005; Arunapuram et al. 2013), or iteratively refining MSA and phylogenetic tree estimates (Liu et al. 2009, 2012).
"Observations, modeling and theory.
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