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IQTree for consensus strategy #23

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chtsai0105 opened this issue Jul 15, 2024 · 0 comments
Open

IQTree for consensus strategy #23

chtsai0105 opened this issue Jul 15, 2024 · 0 comments
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It have been reported that the tree module runs forever when building with IQTree in consensus mode.

After further check, I found the ModelFinder process is quite time-consuming (usually take > 2 hours) even with single MSA file. Haven't tested RAxML but I suspect it also takes similar time to process. In this case, building trees from all the MSAs with IQTree/RAxML in consensus mode seems to be unrealistic.

Potential resolutions:

  1. Looking for parameters that can speed up IQTree/RAxML and apply it when using consensus mode.
  2. Removing IQTree and RAxML from consensus mode.
@chtsai0105 chtsai0105 self-assigned this Jul 15, 2024
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