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- New option
--cf-quartetto write site concordance factors for all resampled quartets to
.cf.quartetfile (requested by Benjamin Rosenzweig and Matt Hahn).
- Site concordance factor (sCF) now works on multifurcating trees.
This version integrate the latest LSD2 version 1.8 that fixes a few issues. Moreover, the outgroup will now be kept in the time tree by default.
- Crash with -bnni option and GHOST model (reported by Miles Zhang and thanks Diep).
- Crash with --sampling option for -bnni and -b (standard bootstrap) (thanks Diep).
--symtest: use the normalised divergence (reported by Peter Foster).
- Binary mixture models do not work as specified (reported by Edward Braun).
- Fix issue #145 in LSD2, update lsd v1.8.1.
- New protein model FLAVI.
This version incorporates the latest LSD2 (v1.7.1) code that fixes a bug and changes some default behaviour such as variance.
--date-cito compute confidence interval of the date estimates under a relaxed clock model.
--clock-sdto set the standard deviation of the lognormal distribution.
--date-outlierto detect and remove outlier (long) branches.
- Hanging in MPI version (reported by @poquirion).
- Duplicated description in site-concordance stat file (reported by Dan Vanderpool).
--redooption semantic is changed to redo both ModelFinder and tree search. Whereas the old behaviour is only redoing tree search while restoring ModelFinder. This old behaviour is now called
- Executable name is now changed to
iqtree2to clearly distinguish with version 1.
- Compilation error when when -DUSE_LSD2=ON is not defined in CMake.
- Compilation error for -DIQTREE_FLAGS=single in CMake.
- Update LSD2 to report error when outgroup taxa are not monophyletic.
- Infer dated time tree via
--dateoption, powered by least square dating (LSD) method. Thank @tothuhien for very quick responses to make this release possible.
Please see http://www.iqtree.org/doc/Dating for how to use this feature.
- Assertion about Eigen::Success, "transformed Q is symmetric", and "eigenvalues are not positive".
- Crash with terrace analysis at the end: turned off by default.
- Rooted input tree is improperly unrooted (reported by Suha Naser).
--subsample-seedoptions to sub-sample a number of partitions.
- Ability to read a partition nexus file with both DATA and SETS blocks.
- New set of Q matrices for QMaker manuscript.
--scfprint an annotated nexus tree file
.cf.tree.nexviewable in FigTree.
- Accept bar character in taxon names (requested by @rambaut).
v2.0-rc1 release candidate 2.0-rc1
This is the release candidate for the major release of the IQ-TREE version 2.
- New option
--subsampleto subsample a number of partitions.
- New option
--subsample-seedto set the random seed for