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Hi,
thank you for the wonderful program,
I sucsessfully use its algorithms rewritten in C++ in my work.
I would like to draw your attention to the fact that the argmax_clusters function works very inefficiently with methods "xxx_clade". Each such method, at first, calculates the required distances when traversing the tree without using the "threshold" parameter, and then the another algorithm (the same in all "xxx_clade" methods) performs clustering with this parameter.
If you separate the distance calculation (one times) and clustering in cycle with "threshold" stepping of these methods in the argmax_clusters, you will get at least double/triple acceleration of this function, and when using the min_clusters_threshold_med_clade method, this acceleration is even difficult to estimate.
If you find time for such optimization, users will be very grateful to you.
The text was updated successfully, but these errors were encountered:
Hi,
thank you for the wonderful program,
I sucsessfully use its algorithms rewritten in C++ in my work.
I would like to draw your attention to the fact that the argmax_clusters function works very inefficiently with methods "xxx_clade". Each such method, at first, calculates the required distances when traversing the tree without using the "threshold" parameter, and then the another algorithm (the same in all "xxx_clade" methods) performs clustering with this parameter.
If you separate the distance calculation (one times) and clustering in cycle with "threshold" stepping of these methods in the argmax_clusters, you will get at least double/triple acceleration of this function, and when using the min_clusters_threshold_med_clade method, this acceleration is even difficult to estimate.
If you find time for such optimization, users will be very grateful to you.
The text was updated successfully, but these errors were encountered: