Beta version 1.7-beta

Notable features:

• -spu PARTITION_FILE to perform separate phylogenetic analysis for each partition.
• NONREV for general non-reversible models.
• --symtest to perform Symmetry Test as of Jermiin et al.
• --terrace to check if ML tree lies on a phylogenetic terrace (code from https://github.com/terraphast)
• --tbe to perform transfer bootstrap expectation (code from https://github.com/evolbioinfo/booster)

New options:

• -sup2 to map support values from a set of trees with unequal taxon sets onto a target tree.
• -rf2 to compute Robinson-Foulds distance between two sets of trees with unequal taxon sets.
• --link-model to link substitution models across partitions.
• --root-move-dist to optimise rooting position up to a certain distance (default: 2).
• --init-model to specify initial rate matrix.
• --loop-model to specify number of loop iterations for partition model optimisation (default: 10).
• --no-seq-comp to disable sequence composition test.
• --symtest-remove-bad to do --symtest and remove bad partitions.

Patch version 1.6.7.1

• 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)

IQ-TREE version 1.6.7

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).

Beta version 1.6.7.a

Bugfixes:

• Checkpointing issue in ModelFinder for mixture models causing incorrect likelihoods with e.g. -madd C10 (reported by Juergen Strassert).
• Checkpointing Lie Markov models.

IQ-TREE version 1.6.6

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).

Beta version 1.6.6.c

This beta version includes all bug fixes from 1.6.6.a and 1.6.6.b and additionally:

• Freezing caused by old Intel OpenMP library on Mac (possibly Linux as well) (reported by David Maddison).
• Too strict assertion about one applied NNI (possibly fix Karen's bug report).
• Error message when specifying mixture with GHOST model (reported by Anja Spang).

Beta version 1.6.6.b

NOTE: Do not use this beta version unless you are asked to test it.

Bugfixes:

• Memory leak in reading NEXUS alignment (possibly fix --runs option reported by David Maddison).
• Crash with resampling strategy (-bsam) for standard bootstrap (-b) and jackknife (-j option).
• Standard bootstrap with 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).

Bugfixes from v1.6.6.a:

• Issue with internal tree node names changed from slash to underscore (reported by JP Flandrois).
• ASSERT with protein mixture models (reported by Giddy Landan).
• Disallow specifying both --runs with -lmap option (reported by Giap Nguyen)
• Reading nexus composite characters for non-DNA data (reported by a web user)
• Support amino-acid O (22nd amino-acid), which is regarded as missing data (reported by Cuong).
• Initialising free-rate model, which may create negative rates in rare cases (reported by Paul Frandsen).

Beta version 1.6.6.a

NOTE: Do not use this beta version unless you are asked to test it.

Bugfixes:

• Issue with internal tree node names changed from slash to underscore (reported by JP Flandrois).
• ASSERT with protein mixture models (reported by Giddy Landan).
• Disallow specifying both --runs with -lmap option (reported by Giap Nguyen)
• Reading nexus composite characters for non-DNA data (reported by a web user)
• Support amino-acid O (22nd amino-acid), which is regarded as missing data (reported by Cuong).
• Initialising free-rate model, which may create negative rates in rare cases (reported by Paul Frandsen).

IQ-TREE version 1.6.5

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).

IQ-TREE version 1.6.4

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).