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Widely divergent topologies have been suggested based on various data sets and methods.
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The close relationship between WOVitA1 and WOVitB was further confirmed by a phylogenetic analysis of phage genes showing divergent phage gene topologies from the Wolbachia protein-coding genes (supplementary fig. S1, Supplementary Material online).
First, some evolutionary processes such as horizontal gene transfer or gene duplication followed by differential gene loss may result in a divergent gene tree topology as compared to the actual species phylogeny.
In M. brevicollis the Nme7 protein is structurally highly divergent as shown but the topology of the phylogenetic tree (Figure 4A) and displays a unique and incomplete domain (Figure 4B).
These models instead yielded a tree topology where the divergent aplousobranch families (Polyclinidae, Polycitoridae and Didemnidae) clustered within Thaliacea to the exclusion of the Clavelinidae species.
An example of the residues predicted to be functionally divergent was mapped onto the topology models of the Group 7/9 members.
The p-value heatmap (Figure 3B) indicates that most gene trees showed divergent histories (depicted as groups of topologies with dissimilar p-value patterns) that are most likely due to horizontal gene transfer.
Specific details of the bundles differ, especially the surface residues, but the helical bundle topologies are identical, suggesting divergent evolution from an ancient exocyst ancestor protein for these four exocyst components [3], [15].
Both maximum likelihood and Bayesian analyses produced identical topologies showing two highly divergent and strongly supported monophyletic lineages.
Residues predicted to be functionally divergent in anoctamins were mapped onto topology model of human anoctamin 1.
Residues predicted to be functionally divergent in bestrophin, were mapped onto topology models of human bestrophins 2 and 4, respectively.
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