IQ TREE Versions Save

New features:

• New option --cf-quartet to write site concordance factors for all resampled quartets to .cf.quartet file (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.

Bugfixes:

• 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 features:

• 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.

New options:

• --date-ci to compute confidence interval of the date estimates under a relaxed clock model. --clock-sd to set the standard deviation of the lognormal distribution.
• --date-outlier to detect and remove outlier (long) branches.

Other fixes:

• Hanging in MPI version (reported by @poquirion).
• Duplicated description in site-concordance stat file (reported by Dan Vanderpool).

Important changes:

• --redo option 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 --redo-tree.
• Executable name is now changed to iqtree2 to clearly distinguish with version 1.

Hot fixes:

• 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.

New features:

• Infer dated time tree via --date option, 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.

Bugfixes:

• 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).

New features:

• --subsample and --subsample-seed options 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.
• --gcf and --scf print an annotated nexus tree file .cf.tree.nex viewable in FigTree.
• Accept bar character in taxon names (requested by @rambaut).

This is the release candidate for the major release of the IQ-TREE version 2.

• New option --subsample to subsample a number of partitions.
• New option --subsample-seed to set the random seed for --subsample.

Bugfixes:

• Crash "transformed Q is symmetric" (reported by Rob Lanfear and others).
• Optimisation of linked substitution model across partitions (reported by Cuong Dang).
• Crash with rooted input trees for non-reversible models (reported by Cuong Dang).
• Compile error with 32-bit Windows.