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Consistent with the original evolutionary definition of orthology, it would probably be best to restrict this further to the most probable ancestral copy number, whose function was probably conserved.
For the analysis of the rate of irreversibility, we used only the mammalian tree because of a higher fraction of the most probable ancestral states in that tree with a high posterior probability in the lineage leading up to humans (98.7% of all states had >0.95 posterior probability).
The likelihood and Bayesian ancestral reconstruction methodology that we use produces the most probable ancestral sequence given certain evolutionary model assumptions, along with a posterior probability for alternative amino acids at each position.
By letting the model evolve along the branches of the phylogeny, which here represent the time since cladogenesis (Fig. 4b), we can estimate the rates (probability) of occurrence of the biogeographic processes (DAB, DBA, EA, EB) and infer the most probable ancestral ranges at every cladogenetic event (Fig. 4c; Sanmartín 2010).
Asia and North America are the most probable ancestral areas for all Sclerodermatineae, and Pinaceae and angiosperms (primarily rosids) are the most probable ancestral hosts.
We also used the tcs software (Clement et al. 2000) to identify the most probable ancestral haplotypes.
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The most probable local ancestral locations are found by maximizing arg max Z P (Z | h ; X ∗ ) = arg max Z P (h | Z ; X ∗ ) P (Z ) which can be efficiently solved by the Viterbi algorithm (Viterbi 2006).
The most probable local ancestral states are obtained by maximizing arg max Z P (Z | g ; X ∗, Y ∗ ) = arg max Z P (g | Z ; X ∗, Y ∗ ) P (Z ) which can be efficiently solved by the Viterbi algorithm (Viterbi, 2006).
To investigate the genetic behavior and genome structure of the peanut, we have over some years built up data sets centered around the two most probable diploid ancestral species of cultivated peanut, an induced allotetraploid derived from them, cultivated peanut, and RILs derived from a cross between them (Shirasawa et al. 2013; Bertioli et al. 2014; unpublished data).
The clustering analysis identified K = 5 as the most probable number of ancestral clusters; among the Italian breeds, Girgentana and Maltese revealed a good internal cohesion, whereas Argentata dell'Etna, Messinese, Capra dell'Aspromonte and Rossa Mediterranea showed a rather high rate of admixture.
It seems most probable that the ancestral NCLDV encoded both subunits of polyA polymerase, and subsequently, most viruses have lost the gene for the regulatory subunit and some have lost both genes.
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