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Table 2 Effect of tightening the EM convergence criteria for the PROT3 benchmark. The "mininc" parameter is the minimum fractional log-likelihood increase per iteration of EM. Accuracies for the gtjxyl benchmark alignment are reported, along with log-likelihoods. See Table 1 for additional notation.

From: XRate: a fast prototyping, training and annotation tool for phylo-grammars

mininc Runtime/min Acc(gtjxyl) log2 P(A, D|θ D ) log2 P(D|θ D ) log2 P(A|D, θ D )
le-3 14 64.1 -2696469 -2549947 -146522
le-4 35 64.7 -2686598 -2539908 -146690
le-5 84 68.0 -2682667 -2536849 -145818