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This tree is typically either selected randomly, determined by the user, or is built using a heuristic.
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].
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However, package managers are often built using a monolithic architecture and hard-wired and ad-hoc dependency solvers implementing some customized heuristics.
A supertree was built using heuristic searches in Clann (Creevey and McInerney, 2005).
The best alternatives were built using constrained ML heuristic searches.
Then, the RH maps were built using the Lin-kernighan heuristic based commands: lkh, lkhn, lkhl, lkhd, lkhocb and lkhocbn.
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.
Experiments with a proof-of-concept implementation, built using Java Pathfinder and WEKA, demonstrate that this heuristic locates bugs faster and more reliably than a conventional counterpart.
For leopard cats, a separate Maximum-Likelihood tree based on a heuristic search and 500 bootstrap replicates, as well as a Neighbor-Joining tree with Jukes-Cantor distances and 1000 bootstrap replicates were built using PAUP* with 575 bp of cytochrome b and sequences included from the earlier study [23], using the fishing cat as outgroup.
We carry out the normalization using a heuristic way.
Parsimony analyses were conducted using a heuristic search strategy.
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