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Second, INTREPID is computationally efficient, making it useful in large-scale application, and allowing it to be used on large datasets.
The computational speed of the algorithm allows it to be used on large datasets.
Most other authors have used simpler approaches, which could eventually be used on large datasets.
To enable the use of HMC on complex models in high-dimensions, we have developed a GPU-based sampling scheme that allows neural network models to be used on large datasets [ 25].
This means that while our method can handle datasets of a few thousand markers and individuals, it cannot be efficiently used on large datasets of hundreds of thousands of markers.
This optimization problem is NP-hard (Jiang et al., 2001), and so ASTRAL has two versions: an exact version that is guaranteed to return the globally optimal tree, and a heuristic version that can be used on large datasets.
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This indicates that the GCPV method does group together functionally related gene clusters effectively and can be used on larger datasets with gene clusters that are not well-characterized.
One critical issue during development was to make the implementation efficient for use on large datasets.
Statistically consistent co-estimation of gene trees and species trees is possible [ 10, 11], but these methods are much more computationally intensive than the most popular summary methods and so are not used on large-scale phylogenomic datasets [ 12- 14].
One unifying feature among the many companies that became known as genomics firms and were included in our database was that all or a substantial fraction of their business plans hinged on use of large datasets on several or many genes, emerging DNA technologies of sequencing, novel methods of DNA detection, or interpretation of information based on DNA sequence or structure.
Although we were not chiefly concerned with the runtime of the methodology, our prototype assembler can be used on fairly large datasets.
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