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The third row indicates the percentage of these families where MowgliNNI proposes a modified tree of lower reconciliation cost.
Only in 21.5% of cases did TreeFix-DTL output a gene tree with lower reconciliation cost than the true tree.
To implement this strategy, TreeFix-DTL performs local search starting with the given ML gene tree and successively finds statistically equivalent gene trees that have a lower reconciliation cost.
Separately, MowgliNNI was used to search for an alternative gene tree topology (G NNI ) of lower reconciliation cost, along with one of its most parsimonious evolutionary history (R NNI ).
For gene families with a lower reconciliation cost (24% of all families), we counted the number of events of each kind (D, T, L ) inferred by Mowgli and MowgliNNI.
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MowgliNNI allowed to change the gene tree, hence to lower the reconciliation cost, in 24% of the ≈30,000 families.
The fact that reconciliation lowers the threshold for passing legislation does not mean it's an undemocratic tool, particularly in a situation where the process is the enemy.
The BSC protocol incorporates two subprotocols, bounded set reconciliation and lower bound agreement, and uses those to realize an efficient Byzantine fault-tolerant variant of ByzConsensus.
In that setting, the parsimony approach is then to prefer a reconciliation of lower cost.
Given such a lower bound, the bounded set reconciliation protocol must detect faulty participants in (O k + (m - mathcal {L}))).
All peers reconcile their initial set with each other, using pairwise bounded set reconciliation using a lower bound of (mathcal {L} = 0).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com