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The likelihood calculation involves 2D integrals, which were calculated using Mathematica.
Probabilities were calculated by using the assignment likelihood calculation of Rannala and Mountain (1997), with resampling based on the simulation algorithm of Paetkau et al. (2004).
dos Reis, M. & Yang, Z. Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times.
Accounting for this correlation is important for phylogenetic inference because it affects the likelihood calculation.
PLANET also exposes a commit likelihood calculation for transactions, which can be utilized for user-defined commits as well as admission control.
However, when data from multiple loci on the same chromosome are used, genetic linkage can affect the final likelihood calculation.
In our paper, we show that we can reduce the likelihood calculation to a binary pairwise MRF defined on the association graph between the RARG and ARG (Figure below).
The likelihood calculation uses two evolutionary models simultaneously for different parts of the sequence: a paired-site model for the paired sites and a single-site model for the unpaired sites.
Compared with a previous profile score that was based on the log-odds likelihood calculation, the correlation between predicted and experimental ΔΔG of single-site mutations is increased in this approach from 0.33 to 0.68.
Execution time comparison in likelihood calculation step.
Execution time comparison in resampling step Fig. 6 Likelihood calculation.
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