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We performed benchmarking tests on a large set of nucleic acid and protein sequences For protein benchmarks we used the benchmark database BALIBASE 3 and an updated release of the database IRMBASE 2 for assessing the quality on globally and locally related sequences, respectively.
Parameter optimization presents a challenge to independently performed benchmarking studies.
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Finally, we perform benchmarking experiments with Mosco, the results of which indicate small overhead and high scalability.
To validate the model we have implemented it in the Squeak Smalltalk environment, and performed benchmarks.
We performed benchmark studies on the molecular geometry, electron properties and vibrational analysis of imidazole using semi-empirical, density functional theory and post Hartree-Fock methods.
We performed benchmarks of phylogenetic grammar-based ncRNA gene prediction, experimenting with eight different models of structural evolution and two different programs for genome alignment.
SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks.
We performed benchmarks for DNA as well as for protein alignment.
The challenges we have encountered whilst attempting to perform benchmarking of patent chemistry databases that automatically extract chemical structures from patents highlights that more needs to be done to make this task easier.
In the recent paper by Lepage et al. [ 21], the authors perform benchmarking of relaxed clock models.
This highlights the need for a detailed understanding of any chosen data and analysis pipeline and the value of performing benchmarking with simulated data.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com