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equal to the difference in the number of free parameters allowed by the two models (i.e., alternative [= full model] versus null [= constrained model] hypotheses) All models were fitted by ML nonlinear optimization across a sample of 1,000 of our Beast trees, using a heuristic starting point based (by default) on the state-independent BD model.
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A Maximum-Likelihood (ML) tree was built using a heuristic search starting from a neighbour-joining tree and a tree bisection reconnection (TBR) algorithm for branch swapping, with random addition of sequences in PAUP* 4.0 [ 74].
This is done using a heuristic search strategy starting from a randomly generated motif.
The dataset containing only phenotypic data was analyzed in PAUP* (v.4.0b10) [ 74] using a heuristic search algorithm with starting trees built using random stepwise addition with tree bisection and reconnection (TBR) branch swapping and twenty random addition sequence replicates.
Optimal trees were found using a heuristic search with the following options: tree-bisection-reconnection (TBR) branch-swapping, MulTrees option in effect, starting tree obtained via stepwise addition, trees held at each step = 5, and MaxTrees = 100.
Tree searches were performed using an heuristic search method (options: set to hold 10 000 trees, 1000 replications, 100 starting tree replication, multiple TBR + TBR search strategy).
Furthermore, this algorithm uses a heuristic-based approach: by starting with the hierarchical scaffold algorithm (HierS; designed and implemented in-house by Jeremy Yang), Dr Ursu's method prunes the cluster search space using HierS heuristics and then applies approximate or exact clique detection algorithms based on molecule size.
FastTree 1.0 uses a heuristic variant of neighbor joining [3], [4] to quickly find a starting tree and uses nearest-neighbor interchanges (NNIs) to refine the topology.
Starting with small data sets, students can practice drawing trees by hand and then use a heuristic computer search to generate the most parsimonious tree with a larger set of data.
A good detective uses good heuristics, starting with proven questions, such as: What was the cause of death?
For Nu we use a heuristic model.
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