News

IQ-TREE version 1.6.10

Feb 19, 2019 Release

Bugfixes:

  • Crash with edge-unlinked model (-sp) and -bnni option (reported by Mark Miller).
Download latest version 1.6.10

IQ-TREE version 1.6.9

Dec 20, 2018 Release

Bugfixes:

  • IMPORTANT: Incorrect AU test p-values with partition models, introduced in v1.6.8 (reported by Ales Bucek).
  • Crash in ModelFinder when having codon partitions with different genetic codes (reported by Morgan Jackson).
  • Crash with multiple runs option (--runs) and -bnni (reported by Vanessa Vera Fain).

Other changes:

  • Better error checking for nexus partition file to prevent mis-specifying comma and semi-colon (reported by Denis Jacob Machado).
  • Safe writing checkpoint file via a temporary file (reported by Giuseppe Aprea and thanks Heiko).
  • -rcluster-max activates relaxed clustering algorithm without having to specify -rcluster.
  • --no-outfiles suppress .treefile as expected (reported by Cecile Ane).
Download version 1.6.9 from GitHub

IQ-TREE version 1.6.8

Oct 28, 2018 Release

Important change:

Bugfixes:

  • Crash with model selection for mixed data type (reported by Paul Frandsen).
  • Crash with model selection when partitions <= 2 (reported by Michele Leocadio).
  • Reading non-reversible models from file.
  • Error message “A taxon has no name” to “Redundant double-bracket”.
Download version 1.6.8 from GitHub

IQ-TREE version 1.6.7.1

Sep 7, 2018 Release

  • Show more precision in log likelihood with --show-lh (thanks Benjamin Redelings)
  • Reimplement -tina and -st MULTI option (requested by Ingo Ebersberger)

Bugfixes:

  • Crash at the end with --runs and partition model (reported by David Maddison)
Download version 1.6.7.1 from GitHub

IQ-TREE version 1.6.7

Aug 23, 2018 Release

Important changes:

  • Temporarily disable AU test due to unresolved numerical issue when bp-rell are all zeros.

Bugfixes:

  • Checkpointing issue in ModelFinder for mixture models causing incorrect likelihoods with e.g. -madd C10 (reported by Juergen Strassert).
  • Checkpointing Lie Markov models.
  • (v1.6.6) Incomplete parsing of site positions of partition file (reported by Alexey Kozlov).
  • Parsing polymorphic states from NEXUS file (reported by Steven Heritage).
  • Use of only 1 thread when #partitions < #cores (reported by Alexey Kozlov).
  • Double RAM usage for -bnni option (reported by Juergen Strassert).
  • Over-bound for optimizeTreeLengthScaling causing too long branch lengths in extreme cases (reported by vikaszsi77).
  • Exclude ORDERED model by default for morphological data due to frequent numerical underflow.
  • (v1.6) -m ..MERGE.. wrong concatenateAlignments with missing data (reported by David Dunchene).
  • Error message instead of crash when using -bsam with non-partition model (reported by Sarah Jensen).
Download version 1.6.7 from GitHub

IQ-TREE version 1.6.6

Jul 1, 2018 Release

This version contains a number of bugfixes and is highly recommended for all users.

Bugfixes:

  • Issue with internal tree node names changed from slash to underscore (reported by JP Flandrois).
  • Wrong FREQ_UNKNOWN assertion with protein mixture models, e.g. LG4X (reported by Giddy Landan).
  • Disallow specifying both --runs with -lmap option (reported by Giap Nguyen).
  • Reading nexus polymorphic characters for non-DNA data (reported by a web user).
  • Amino-acid O (22nd amino-acid) is accepted as missing data (reported by Cuong Dang).
  • Negative initial free-rates in rare cases (reported by Paul Frandsen).
  • Memory leak in reading NEXUS alignment.
  • Crash with resampling strategy (-bsam) for standard bootstrap (-b) and jackknife (-j option).
  • Crash with standard bootstrap and partition merging (-m ...MERGE) (reported by Guoqing Li).
  • Wrong error with codon models and -t RANDOM (reported by Karen Meusemann).
  • Parsing error with blank chars in partition file (reported by David Maddison).
  • Freezing caused by old Intel OpenMP library (reported by David Maddison).
  • Too strict assertion about one applied NNI (reported by Karen Meusemann).
  • Error message when specifying mixture with GHOST model (reported by Anja Spang).
Download version 1.6.6 from GitHub

IQ-TREE version 1.6.5

May 8, 2018 Release

Bugfixes:

  • GTR20 protein model does not optimise rate parameters.
  • Replace odd characters in taxon names in tree file by underscore as done with alignment file (issue #31).
  • Replace odd characters in taxon names in cluster file by underscore (issue #54).
  • Crash with combination of bootstrap (-b option), partition model (-spp) and model testing (-m TEST) at the phase of analysing original alignment (reported by paul.madeira).
Download version 1.6.5 from GitHub

IQ-TREE version 1.6.4

Apr 30, 2018 Release

News:

  • New option --runs to perform multiple tree searches (issue #64 requested by David Maddison). This is motivated by a recent evaluation (Zhou et al. 2018) showing that 10 independent runs outperformed single run in terms of likelihood maximisation.
  • Print branch lengths scaled in number of substitutions for PoMo models.
  • Support specifying 6 GTR rates and G-T rate to be zero from command line (requested by Ben Redelings).
  • New option --show-lh to compute tree log-likelihood without parameter optimisation (issue #67).

Bugfixes:

  • Fix compilation with gcc 4.8.
  • Incorrect parsing +P for PoMo model string (thanks Carolin Kosiol).
  • Issue #66: Incorrect frequency mixture model when coupled with GTR20 (reported by Dominik Schrempf).
  • .ufboot trees file contains partial branch supports by combination of -bb and -alrt (reported by Guifre Torruella Cortes).
  • Crash in likelihood computation for +ASC model when some states are rare (reported by Paul Madeira).
  • Numerical instability for codon models by reducing upper bound of omega/kappa from 100 to 50 (reported by Aleksas Lab).
  • Crash reading DNA model from file (reported by Benjamin Redelings).
  • Crash with -z option with rooted trees in the presence of identical sequences (reported by cjp1043).
Download version 1.6.4 from GitHub

IQ-TREE version 1.6.3

Mar 22, 2018 Release

This version improves software stability and highly recommended to update for all users.

Bugfixes:

  • Abort in ModelFinder when a user tree is supplied via -t option.
  • Erroneous message “leaves and taxa_set do not match” by rooted user tree (-t) and partition model (reported by Dieter Waechter).
  • Abort in ModelFinder by -sp option (edge-unlinked) and -mtree.
  • Error-checking partition with identical names.
  • Crash with rooted user trees via -z option.
  • Change ERROR about Too many iterations in tqli to WARNING.
  • Abort with combination of -nt AUTO and -mtree (reported by Mark Miller).
  • Crash with -bnni and -spp by temporarily turning on NNI5 instead of NNI1 (originally reported by Xiaofan).
  • Quitting by mixed data types (reported by Stephen Baca).
  • Crash with numerical underflow for lh-branch (reported by Karen Siu Ting).

New features:

  • -ntmax option to specify maximum number of threads by -nt AUTO option (requested by @sjspielman).
  • SH-aLRT test is now parallelised over multiple cores (requested by Heiner Kuhl).
  • Support GTR model for multistate data (requested by Sergio Andres Munoz Gomez).
  • Support jackknife with new option -j (requested by Emmanuel Toussaint).
  • New option -version to display version number (requested by David Maddison).
Download version 1.6.3 from GitHub

IQ-TREE version 1.6.2

Mar 1, 2018 Release

Bugfixes:

  • Fix a thread-unsafe bug during partition merging of ModelFinder (reported by Karen Meusemann and Marianne)
  • Fix infinite hanging by LG+C10 or similar models (reported by Craig Herbold)
  • Fix parsing -net option (reported by Cameron Weadick)
  • Fix error message for -fast and -bb

New features:

  • Support reading non-reversible protein Q matrix from a file.
  • New option --write-branches to write branch lengths of tree (and partition trees) into .branches.csv file (requested by Rob Lanfear)
  • Allow -o option to specify a comma-separated list of outgroup taxa (requested by Andrew Roger)
Download version 1.6.2 from GitHub