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Releases: Cibiv/IQ-TREE

Version 2.0.7

17 Jun 13:15
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Version 2.0.7 Pre-release
Pre-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.

Version 2.0.6

12 Jun 02:25
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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.

Version 2.0.5

15 May 08:45
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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).

IQ-TREE version 2.0.4

27 Apr 02:53
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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.

IQ-TREE version 2.0.3

24 Apr 02:35
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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.

Release candidate v2.0-rc2

27 Mar 14:10
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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).

Release candidate 2.0-rc1

21 Nov 11:58
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v2.0-rc1

release candidate 2.0-rc1

Version 2.0-rc release candidate

20 Nov 00:00
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This is the release candidate for the major release of the IQ-TREE version 2.

Beta version 1.7-beta18

30 Oct 01:28
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  • New option --subsample to subsample a number of partitions.
  • New option --subsample-seed to set the random seed for --subsample.

Beta version 1.7-beta17

22 Oct 00:41
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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.