What's new in jModelTest 2.1.7
Feb 20, 2015
- Fixed bug with special characters in paths
- Added initial check of PhyML binaries
- Added notification in case AICc produces negative values
- Allow for environment variables on configuration file
- Fixed minor bug in console version. NNI tree search operation was taken as default for ML starting tree, instead of BEST.
New in jModelTest 2.1.6 (Aug 14, 2014)
- Added confirmation window when cancelling running jobs in the GUI
- Added automatic checkpointing files generation
- Added "-ckp" argument for loading checkpointing files
New in jModelTest 2.1.5 (Aug 14, 2014)
- Fixed bug with computation of JC model for "fixed" topology
- Fixed bug with DT criterion computation
- Added "-n" argument for naming executions (the name is included in the log filenames)
- Added "-getphylip" argument for converting alignments into PHYLIP format with ALTER
- Fixed bug in PhyML logging in GUI. Added a unique ID for every model in the log file
- Added PAUP* block into log files if required ("-w" argument)
- Added more verbose error messages
New in jModelTest 2.1.4 (Aug 14, 2014)
- Added phyml auto-logging.
- Added phyml command lines for best-fit models.
- Added phyml log tab in the GUI.
- Removed sample size modes (and "-n" argument). Sample size is fixed to alignment size.
- Fixed bug with relative paths when calling from a different path.
- Fixed typos in the GUI.
New in jModelTest 2.1.3 (Feb 8, 2014)
- Fixed bug with PAUP* command block.
- Added the possibility to change Inforation Criterion used with the clustering algorithm for the 203 matrices.
- Changed "-o" argument for the hypothesis order into "-O"
- Added "-o" argument for forwarding the standard output to a file: -o FILENAME
New in jModelTest 2.1.2 (Feb 8, 2014)
- Fixed bug in paths with whitespaces.
- Updated PhyML binaries.
New in jModelTest 2.1.1 (Feb 8, 2014)
- Fixed bug with hLRT selection when attempting to use a user-defined topology.
New in jModelTest 2.1 (Feb 8, 2014)
- Major updates:
- Exhaustive GTR submodels: All the 203 different partitions of the GTR rate matrix can be included in the candidate set of models. When combined with rate variation (+I,+G, +I+G) and equal/unequal base frequencies the total number of possible models is 203 x 8 = 1624.
- Hill climbing hierarchical clustering: Calculating the likelihood score for a large number of models can be extremely time-consuming. This hill-climbing algorithm implements a hierarchical clustering to search for the best-fit models within the full set of 1624 models, but optimizing at most 288 models while maintaining model selection accuracy.
- Heuristic filtering: Heuristic reduction of the candidate models set based on a similarity filtering threshold among the GTR rates and the estimates of among-site rate variation.
- Absolute model fit: Information criterion distances can be calculated for the best-fit model against the unconstrained multinomial model (based on site pattern frequencies). This is computed by default when the alignment does not contain missing data/ambiguities, but can also be approximated otherwise.
- Topological summary: Tree topologies supported by the different candidate models are summarized in the html log, including confidence intervals constructed from cumulative models weights, plus Robinson-Foulds and Euclidean distances to the best-fit tree for each.
- Minor updates:
- Corrected a bug in the fixed BIONJ-JC starting topology. F81+I+G was executed instead of JC.
- "Best" is now the default tree search operation instead of NNI. "Best" computes both NNI and SPR algorithms and selects the best of them.
- User can select the number of threads from GUI.
New in jModelTest 2.0.2 (Feb 8, 2014)
- Added a selection summary at the end of the console output.
- Corrected the table header in the DT results frame (sorting).
- Corrected a bug in DT Criterion where selection could not take place with large alignments.
- Corrected a bug with command console version, where the execution crashed with certain arguments.
- Unified LOCALE for English format.
New in jModelTest 2.0.1 (Feb 8, 2014)
- Improved thread scheduling algorithm.
- OpenMP phyml patch for hybrid execution.
- New argument (machinesfile) for hybrid execution on heterogeneous architectures, or heterogeneous resources distribution.