Releases: iqtree/iqtree2
v2.2.2.2
This release integrates the latest implementation of FunDi model (v2.2.2.1) and the following updates in AliSim (AliSim-HPC).
- Bugs fixed:
- Rate heterogeneity across mixture components in a mixture model.
- Avoid generating a random negative state frequency.
- Normalize state frequencies even if the total of them is almost 1 (e.g, 0.9999998)
- Some improvements in implementation.
v2.2.2.1
Beta version with FunDi model
To estimate FunDi branch length for a given rho (e.g. 0.1) and a fixed tree topology:
iqtree2 -s ALN_FILE -m MODEL -te TREE_FILE --fundi tax1,tax2,...,taxK,0.1
To estimate both FunDi branch length and rho:
iqtree2 -s ALN_FILE -m MODEL -te TREE_FILE --fundi tax1,tax2,...,taxK,estimate
If a user tree is not provided with -te option, IQ-TREE will first estimate a tree under MODEL without FunDi, and then go on to estimate the FunDi parameters.
If a model is not provided via -m option, ModelFinder will be invoked to find the best-fit model.
Results are currently printed to screen and log file:
...
Optimizing FunDi model parameters...
Best FunDi parameter rho: 0.107
Best FunDi central branch length: 0.131
FunDi log-likelihood: -118799.390
Time taken to optimize FunDi model: 0.013 sec
...
v2.2.0.8.mix
This is a pre-release supporting Mixtures Across Sites and Trees (MAST) model.
User manual for the MAST model: https://github.com/iqtree/iqtree2/wiki/Complex-Models#multitree-models
Fixed the bug which happened when using the option "-wspm" with incorrect values inside the .siteprob file.
Modified the likelihood calculation to support large trees with many taxa.
v2.2.0.8
Introduce AliSim-HPC, a parallel version of AliSim using OpenMP and MPI.
For a comprehensive user manual, please see https://github.com/iqtree/iqtree2/wiki/AliSim#parallel-sequence-simulations.
v2.2.2
New option --scfl for site concordance factor using likelihood. See http://www.iqtree.org/doc/Concordance-Factor for usage guide.
Version 2.2.0.7
Fixed the issue of repeating to examine the optimal number of threads when using an option -T AUTO
Version 2.2.0.6
Fixed the issue when there is more than one data type along the partitions with duplicate sequences.
Version 2.2.0.7.mix
This is a pre-release supporting Mixtures Across Sites and Trees (MAST) model
User manual for the MAST model: https://github.com/iqtree/iqtree2/wiki/Complex-Models#multitree-models
Version 2.2.0.5
Incorporate all bugs fixed.