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Confidence was examined using bootstrapping (BS) with 1000 replicates and the heuristic option with 100 RAS per pseudo replicate.
For DNA sequences, distances and the molecular tree were computed with the DNAML algorithm with the global rearrangements heuristic option of PHYLIP.
Searches for the MP tree(s) run using the full heuristic option with 10 random replicates and for ML trees the fast stepwise addition option was used.
In MP analysis, trees were searched with the full heuristic option and optimization was performed by branch-swapping using tree bisection and reconnection; in ML-distance analysis, trees were searched with the neighbour-joining search setting.
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In addition to exploring heuristic options, our ongoing work is also aimed at explicitly balancing the cost of reasoning against the quality of solution (See Section 6).
The maximum-parsimony (MP) analysis was applied to MOR, molecular, and combined data matrices (NONA version 2.0 [ 67]: heuristics, option "hold10000 munconstrained100", unconsearched strategytrategy with TBR branch swapping).
MP analyses were conducted for the entire coding sequence matrix and after excluding third codon positions using a heuristic search option and default options (TBR branch swapping), with the exception of using random stepwise addition repeated 100 times.
Unweighted maximum parsimony was conducted using the heuristic search option and 100 random addition sequences with the tree-bisection-reconnection branch swapping and the MULTREES option on.
Parsimony analysis was conducted with the program PAUP* 4.0b10, using the heuristic search option [63].
We performed the heuristic searches option with tree bisection-reconnection (TBR) branch-swapping under Maximum Parsimony (MP).
Bootstrap values based on 100 re-samplings in ML of the dataset were calculated (TBR, full heuristic search option) [27].
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