IQ-TREE version 1.6.10
Feb 19, 2019 Release
Crash with edge-unlinked model (
-bnni option (reported by Mark Miller).
Download latest version 1.6.10 IQ-TREE version 1.6.9
Dec 20, 2018 Release
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 (
-bnni (reported by Vanessa Vera Fain).
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
--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
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 184.108.40.206
Sep 7, 2018 Release Show more precision in log likelihood with
--show-lh (thanks Benjamin Redelings)
-st MULTI option (requested by Ingo Ebersberger)
Crash at the end with
--runs and partition model (reported by David Maddison)
Download version 220.127.116.11 from GitHub IQ-TREE version 1.6.7
Aug 23, 2018 Release
Temporarily disable AU test due to unresolved numerical issue when bp-rell are all zeros.
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.
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
-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 (
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
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
--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).
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
-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.
Abort in ModelFinder when a user tree is supplied via
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
Error-checking partition with identical names. Crash with rooted user trees via
Change ERROR about
Too many iterations in tqli to WARNING.
Abort with combination of
-nt AUTO and
-mtree (reported by Mark Miller).
-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).
-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).
-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
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)
-net option (reported by Cameron Weadick)
Fix error message for
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)
-o option to specify a comma-separated list of outgroup taxa (requested by Andrew Roger)
Download version 1.6.2 from GitHub