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In the literature, there are only some interesting heuristic analyses like the one proposed by Tsoy in [21].
Regardless, our heuristic analyses should be considered as suggestive of potential demographic and genetic costs and not demonstrative.
Heuristic analyses were performed with 500 random addition of sequences and the TBR algorithm for branch swapping.
Previous heuristic analyses of the three Frankia genomes found more transposase ORFs in regions of each genome lacking synteny with the others [ 5].
In heuristic analyses, some spot quality control is still performed, often in terms of threshold values in observables such as spot size, intensity, background variation, or combinations thereof, which are used to flag spots as missing.
Exhaustive Maximum Likelihood (ML) searches were performed on the two updated translation and transcription fusion datasets, with a few constraints given to undisputable nodes (i.e. supported by BV = 100% in preliminary Neighbor Joining and ML heuristic analyses (not shown)).
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Heuristic ML analyses were conducted with TBR branch swapping (10 random addition replicates), as well as bootstrap analyses with 100 replicates in order to assess the robustness of the clades recovered [ 31].
Heuristic parsimony analyses using the combined rbcL and trnL-F database were performed separately for every unknown gametophyte by including one individual at a time in the analysis.
We applied the seriation heuristic to analyses of both simulated and experimental SAGE data and showed that our approach can be used to effectively identify groups of co-expressed genes, and the relationships among these groups in a robust manner.
Heuristic parsimony analyses were implemented with the computer program PAUP*4.0b10.
For heuristic MP analyses, we used Tree Bisection Reconnection branch swapping, with all characters equally weighted and zero-length branches collapsed.
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