Comments (5)
Just confirming that the tree from the new version seems not be optimised with parsimony at all. The branchlengths are ML branchlengths:
# Most common branchlengths from the May 15th version
> head(sort(a1, decreasing = TRUE))
1e-06 3.37526e-05 6.75068e-05 0.0001012624 0.0001350196 0.0001687783
510267 183840 63644 28247 14205 7798
# Most common branchlengths from the Apr 27th version
> head(sort(a2, decreasing = TRUE))
1e-06 1 2 3 4 5
509419 181840 62675 27831 13876 7583
>
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@JamesBarbetti thanks!
The other odd thing I notice in the new code is that I thought you'd mentioned that you'd turned off all the ML stuff, but it's still calculating ML parameters and branch lengths. So a bug in which pathway (ML vs. Parsimony) is chosen seems likely?
Regardless, if the ML stuff can be turned off completely, it would definitely help. Right now the parsimony code for ~400K sequences uses ~130GB memory, but as soon as we shift to the likelihood part it increases to ~550GB. So switching off likelihood will buy us a lot more scale!
Rob
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We won't continue support such high alignments (Alignment has 410000 sequences with 29628 columns, 29518 distinct patterns) in the main code of IQ-TREE. New version 2.3.4.cmaple should solve it.
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Related Issues (20)
- Ambiguous bases being treated as constant HOT 1
- Help with IQ-TREE HOT 3
- Constraint not compatible with ModelFinder? HOT 5
- Segmentation fault when trying to use lds2 with predefined substitution rates HOT 2
- CMake deprecation warning: Compatibility with CMake < 3.5 will be removed from a future version of CMake.
- Build fails on ARM Mac (macOS 14) with `Error at CMakeLists.txt:701 (add_subdirectory)` HOT 4
- IQtree help string should mention architecture HOT 1
- Cannot find exact build setup used to make the release binaries HOT 1
- auto thread number detection with modelfinder HOT 1
- Compilation failure with GCC 12 HOT 8
- A question that how to gene tree root on my data? HOT 3
- Compliation error HOT 6
- A possible bug? HOT 8
- Enhancement request: Implement +ASC option to speed up MixtureFinder searches on supermatrices lacking constant sites HOT 3
- SIGNAL SEGMENTATION FAULT HOT 2
- Feature request: Generate MrBayes block from IQ-TREE HOT 4
- Error with the constrained tree search HOT 3
- Process stuck in INITIALIZING CANDIDATE TREE SET HOT 3
- ModelSelection with IQTREE 2 v2.3.4 COVID-edition HOT 1
- SIGNAL SEGMENTATION FAULT error (v2.3.4) HOT 5
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