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Applying branch-site models and to post cluster duplication (ωPCD) branches identified sites under positive selection after cluster duplication in paralog groups 1 6, 9 and 13 (Table 4).
Post cluster duplication branches evolved significantly faster (3 27x) than post speciation branches for 10 of 13 paralog groups; the remaining 3 paralog groups had ωPCD > ωPS but the results were not significant (Table 1).
Thus, even though we found evidence of accelerated rates of sequence evolution post cluster duplication, it is unlikely that the d N / d S ratio tests used above would be able to detect positive selection (ω > 1).
To test if there was an increase in the nonsynonymous substitution rate following Hox cluster duplication we used a two ratios model that estimated separate ω's for post cluster duplication (ωPCD) and post speciation (ωPS) branches.
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A.S. and M.B. developed the XenDB database schema, performed the post clustering data analyses and contributed to the manuscript.
Studies were not considered to be post-cluster analyses if the identification of an excess of health effects other than cancer provided the impetus for a study to be undertaken.
Understanding when either error type is preferable will be dependent on the analysis conducted post-clustering.
Cluster 4 - Twenty four hours post infestation Cluster 4 represents the late (L) genes with peak up-regulation at 24 hpi.
Cluster 3 - Six hours post infestation Cluster 3 represents the intermediate (IM) group of genes with peak expression at 6 hpi.
Cluster 6 - Three hours post infestation Cluster 6 represents the early (E) repressed genes with peak repressed expression at 3 hpi.
Cluster 2 - Three hours post infestation Cluster 2 represents the early (E) group of genes showing a peak expression at 3 hpi.
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