What are the best parameters and algorithms to perfom a search for datasets with 500 and 3000 species

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The best search parameters critically depends on the dataset. If you do not know too much about searches it might be better to let the program decide which parameters use during the run. This is done with the driven search in the manu version (Analysis/New Technology search/Driven Search/set initial level). If you set the search to 100 the search will be the most aggresive and time consuming and if set to 1, the least aggresive. The command to do that is xmult with the option level (example xmult= level 7). Here the scales goes from 1 to 10.

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