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Early detection is based on the theory, dating back to the late 19th century, that the disease progresses consistently, beginning with a single rogue cell, growing sequentially and at some invariable point making a lethal leap.
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For amino acid sequences, the MTREV model [ 56] with sites following a discrete gamma distribution and some sites invariable (I) was used.
A general time reversible model (GTR) [ 54] with sites following a discrete gamma distribution and some sites invariable (I) was selected as the best model of nucleotide sequence evolution by Modeltest ver. 3.7 [ 55] using the Akaike information criterion (AIC).
The main reason why time to event data provide a greater challenge is the almost invariable censoring of some observation times, caused by some patients' outcomes remaining unascertained within the study period.
He recalls, for instance, how Ike reacted to the news of Pearl Harbor by making some vegetable soup -- his invariable response to periods of "excessive stress".
The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 9.0566% sites).
The rate variation model allowed for some sites to be evolutionarily invariable.
The GTR model, with some sites assumed to be invariable and with variable sites assumed to follow a discrete gamma distribution (ref. [ 79]; GTR + I + Γ), was selected as the best-fit model of the nucleotide substitution for each partition on the basis of the Akaike Information Criteria (ref. [ 81]; AIC).
The general time-reversible model, with some sites assumed to be invariable and variable sites assumed to follow a discrete gamma distribution (GTR + I + Γ; [ 33]), was selected as the best-fit model of nucleotide substitution by MrModeltest 2.2 http://www.abc.se/~nylander/[ 34].
The general time reversible model with some sites assumed to be invariable and with variable sites assumed to follow a discrete gamma distribution [ref. [ 54]; GTR + I + Γ] was used for model of sequence evolution, as it was selected as best-fitting model with MRMODELTEST (Version 2) [ 55] for each partition except for positions with the RY-coding.
In brief, aligned sequences were analyzed with PAUP* 4.0b10 [ 44] using maximum likelihood (ML) under a general time reversible model of sequence evolution [ 45] with some sites assumed to be invariable, and with rate variation among the remaining sites assumed to follow a gamma distribution [ 46, 47].
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