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Pre-release

@bqminh bqminh released this Jun 17, 2020 · 3 commits to master since this release

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.
Assets 7

@bqminh bqminh released this Jun 12, 2020 · 3 commits to master since this release

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.
Assets 7

@bqminh bqminh released this May 15, 2020 · 3 commits to master since this release

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).
Assets 7

@bqminh bqminh released this Apr 27, 2020 · 3 commits to master since this release

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.
Assets 7

@bqminh bqminh released this Apr 24, 2020 · 8 commits to master since this release

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.

Assets 7
Pre-release

@bqminh bqminh released this Mar 27, 2020 · 8 commits to master since this release

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).
Assets 7

@bqminh bqminh released this Nov 21, 2019 · 8 commits to master since this release

v2.0-rc1

release candidate 2.0-rc1
Assets 7

@bqminh bqminh released this Nov 20, 2019 · 8 commits to master since this release

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

Assets 7
Oct 31, 2019
Merge pull request #110 from fgp/fix-eigen3-include-path
Use include_directories() instead of add_definitions() to set EIGEN3_INCLUDE_DIR
Pre-release

@bqminh bqminh released this Oct 30, 2019 · 8 commits to master since this release

  • New option --subsample to subsample a number of partitions.
  • New option --subsample-seed to set the random seed for --subsample.
Assets 7
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